title: SW480-Ethanol_16hours-rep1


title: hiPSC_EV_3

status: Public on Jun 01 2022

type: SRA

city: Oeiras

first: Ana

middle: Filipa

last: Louro

address: Av. República, Qta. do Marquês Edifício iBET/ITQB

department: Animal Cell Technology Unit

country: Portugal

institute: iBET

description:
Sample 3
SV18531_0003_S21

library_source: transcriptomic

data_processing:
Data was processed through the Genboree exceRpt small RNA-seq Pipeline, Version 4.6.2
Exogenous alignment: endogenous-only; Endogenous Library Order: miRNA, tRNA, piRNA, gencode, circRNA. Within the exceRpt 4.6.2 database the sources for small RNA library mapping are: annotations for miRNAs from miRBAse version 21, tRNAs from gtRNAdb, piRNAs from RNAdb, genome from Gencode version 21 (hg38), CircularRNAs from circBase
Filtering by expression performed with EdgeR (version 3.24.0). Filtering cut-off: CPM equivalent to a minimum of 5 counts
Normalization performed by TMM method using EdgeR
Genome_build: Gencode version 21 (hg38)
Supplementary_files_format_and_content: Tab-delimited text files include Read Count or Read Count Per Million for all Samples corresponding to Genboree exceRpt small RNA-seq Pipeline (4.6.2) output or Trimmed-mean of M-values (TMM) files obtained through EdgeR pipeline

molecule: total RNA

organism: Homo sapiens

source_name: Conditioned Culture Medium

extract_protocol:
Total RNA was isolated from EV samples (N=3 biological replicates corresponding to EV preparations from three independent cultures) using Norgen Biotek Exosomal RNA Isolation Kit (Cat.58000).
microRNA library preparation was performed by PCR amplification using Norgen Biotek Small RNA Library Prep Kit (Cat. 63600) and library quality control was achieved using Bioanalyzer to estimate library size and concentration. Libraries were denatured and diluted to the required concentration and then applied onto the suitable flowcell and sequenced using Illumina NextSeq 500 sequencing platforms
Small RNA-seq

tag: cell line

tag: differentiation stage

value: pluripotent stem cell

tag: sample type

value: EV


title: hiPSC_EV_1

description:
Sample 1
SV18531_0001_S19


title: sBPD, 56

type: RNA

city: Bloomington

first: Patricia

last: Silveyra

email: psilveyr@iu.edu, ptrcslvr@gmail.com

state: Indiana

department: Environmental and Occupational Health

country: USA

institute: Indiana University Bloomington

description:
severe BPD
Sample name: 56

data_processing:
Data were analyzed in Excel using Ct values for each sample,  normalized to global means, and fold changes were calculated using the 2-ΔΔCT method.
Data table shows miRNA Ct values normalized to global mean ΔCt = (Ct_miRNA − Ct_global mean)
Supplementary file non-normalized_data.txt:  raw Ct values.
Supplementary file fold-change.txt:  For fold-change calculations (using the livak method), ΔΔCt based fold-change values were obtained using an average of control sample Ct values (2^-ΔΔCt, where -ΔΔCt = -[ΔCtsample -ΔCtavgcontrol])). A fold change of 25 was considered as cutoff.

label: SYBR Green

source_name: tracheal aspirate

label_protocol: Small RNAs were retro-transcribed from 200 ng of total RNA using the miScript II RT kit (Qiagen). The expression of 1066 human miRNAs was assayed with the Human miRNome miScript® miRNA PCR Array (QIAGEN, MIHS-3216Z).

extract_protocol: MicroRNAs were purified from 0.5 mL of TAs with the Plasma/Serum RNA Purification Kit (Norgen Biotek Corp., Thorold, ON, Canada).

treatment_protocol: Tracheal aspirates were obtained from premature babies with sBPD and BPD-PH. Total RNA was purified from TAs and the expression of 1066 human miRNAs was detected with a PCR array.

tag: developmental stage

value: premature neonate

tag: tissue

value: tracheal aspirate

tag: sbpd

value: yes

tag: bpd-ph

value: no


title: hiPSC_EV_2

description:
Sample 2
SV18531_0002_S20


title: LS174T-Calcitriol_16hours-rep2

city: Edinburgh

first: Peter

middle: G

last: Vaughan-Shaw

address: Crewe Road

department: IGMM

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: limma normexp background correction using negative control probes and quantile normalization using negative and positive control probes

label: biotin

source_name: LS174T cell line

label_protocol: For HT12 analysis, total RNA was converted to double-stranded cDNA, followed by in vitro transcription amplification to generate labelled cRNA (Illumina TotalPrep™ RNA Amplification Kit).

growth_protocol: Established colorectal cancer cell lines were used (SW480, LS174T, SW48, DLD1, HCT116, COLO205, T84, LOVO, VACO425, CaCO-2), cultured under standard conditions . When cells reached 80% confluency, standard cell culture techniques were used for cell passaging and maintenance. Cells were treated with 1α,25-dihydroxyvitamin D3 (calcitriol; Sigma) diluted in 100% ethanol, or ethanol control, once 70% confluence was reached. Harvesting of cells for protein and RNA was routinely performed after 16 hours from addition of calcitriol,

extract_protocol: RNA was extracted from cells and organoids using a proprietary RNA extraction kit (Ribopure kit, Applied Biosystems) according to the manufacturer’s protocol. This process initially involved homogenising samples in 1 mL TRIzol. The homogenates were then incubated for 5 minutes at room temperature to enable the nucleoprotein complexes to completely dissociate. 200 μl of chloroform was added and the tubes vortexed at 2800 rpm for 15 seconds. After 5 minutes’ incubation at room temperature, the homogenate was centrifuged at 12,000 x g for 10 min at 4°C. This separated the homogenate into a lower, red, organic phase (phenol-BCP phase); an interphase; and a colourless, upper, aqueous phase. 400 μl of the aqueous phase was withdrawn to which 200 μl of ethanol was added. The mixture was vortexed at maximum speed for 5 seconds and added to a filter cartridge-collection tube. This was centrifuged at 12,000 x g for 30 seconds at room temperature and the flow-through discarded. Two wash cycles using 500 μl of provided wash solution were undertaken, with a final spin of 12,000 x g for 30 seconds to ensure all wash solution had left the filter. Finally, 50 μl of provided elution buffer was added to the filter cartridge within a new collection tube and spun at 12,000 x g for 30 seconds to elute the RNA.

treatment_protocol: Cell line culture was performed in a class 1 biological safety cabinet.  Tissue culture medium used was Dulbecco's Modified Eagle Medium (high glucose, with L-glutamine; DMEM) (Gibco) supplemented with Foetal Calf Serum (10%), or charcoal-treated FCS (10%, Sigma for treatments) and Penicillin/Streptomycin (100 I.U./mL penicillin and 100 μg/mL streptomycin 1%).

tag: treatment

value: Calcitriol


title: sBPD, 52

description:
severe BPD
Sample name: 52


title: LS174T-Calcitriol_16hours-rep1


title: PMA_6h_06

city: oxford

first: Thomas

last: Jackson

address: weatherall institute of molecular medicine

department: paediatrics

institute: University of Oxford

description:
PMA_6h_06
oxstem_6h.csv
HL-60 cells treated with 10nM PMA for 6h

data_processing:
Quality and adapter trimming were performed using Trim Galore
were mapped to the human genome assembly hg19 using STAR software
The featureCounts function from the Subread package was used to quantify gene expression levels using standard parameters
Genome_build: hg19
Supplementary_files_format_and_content: txt counts table

source_name: HL60 cell line

growth_protocol: HL-60 cell line,

extract_protocol:
Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Samples were treated with indicated novel treatements, positive controls or DMSO controls

value: PMA


title: HOVON95: Newly diagnosed MM_216

city: Rotterdam

first: Mark

last: van Duin

address: Wytemaweg 80

country: Netherlands

institute: Erasmus MC

hyb_protocol: 13 ug of fragmented and biotin labeled cRNA hybridized to the microarray in an Affymetrix GeneChip® Hybridization Oven 645 and washed / stained in Affymetrix GeneChip Fluidics Station FS450DX2v2

scan_protocol: Affymetrix GeneChip® System 3000Dx v.2

data_processing: MAS5.0 (Bioconductor affy package v1.36.2) default values with a trimmed mean target intensity value set to 1500. Values below 30 were truncated.

source_name: bone marrow aspirate

label_protocol: Affymetrix Gene Profiling MDx IVD Expression Reagent Kit in accordance with Affymetrix protocols.

extract_protocol: RNeasy

treatment_protocol: Patients were treatment naive

tag: gender

value: Male

tag: age

value: bone marrow aspirate

tag: disease state

value: multiple myeloma


title: sBPD, 51

description:
severe BPD
Sample name: 51


title: HOVON95: Newly diagnosed MM_215


title: HOVON95: Newly diagnosed MM_214


title: LS174T-Ethanol_16hours-rep3

value: ethanol


title: HOVON95: Newly diagnosed MM_213

value: Female


title: LS174T-Ethanol_16hours-rep2


title: PMA_6h_05

description:
PMA_6h_05
oxstem_6h.csv
HL-60 cells treated with 10nM PMA for 6h


title: BPD+PH, 45

description:
BPD with Pulmonary Hypertension
Sample name: 45


title: sBPD, 48

description:
severe BPD
Sample name: 48


title: PMA_6h_04

description:
PMA_6h_04
oxstem_6h.csv
HL-60 cells treated with 10nM PMA for 6h


title: sBPD, 49

description:
severe BPD
Sample name: 49


title: PMA_6h_02

description:
PMA_6h_02
oxstem_6h.csv
HL-60 cells treated with 10nM PMA for 6h


title: sBPD, 42

description:
severe BPD
Sample name: 42


title: HCT116-Calcitriol_16hours-rep3

source_name: HCT116 cell line


title: HOVON95: Newly diagnosed MM_212


title: BPD+PH, 46

description:
BPD with Pulmonary Hypertension
Sample name: 46


title: HOVON95: Newly diagnosed MM_211


title: PMA_6h_01

description:
PMA_6h_01
oxstem_6h.csv
HL-60 cells treated with 10nM PMA for 6h


title: BPD+PH, 34

description:
BPD with Pulmonary Hypertension
Sample name: 34


title: sBPD, 37

description:
severe BPD
Sample name: 37


title: HOVON95: Newly diagnosed MM_209


title: HOVON95: Newly diagnosed MM_208


title: HOVON95: Newly diagnosed MM_210


title: PMA_6h_03

description:
PMA_6h_03
oxstem_6h.csv
HL-60 cells treated with 10nM PMA for 6h


title: HCT116-Calcitriol_16hours-rep2


title: HCT116-Ethanol_16hours-rep3


title: OX7464_6h_06

description:
OX7464_6h
oxstem_6h.csv
HL-60 cells treated with 1uM OXS007464 for 6h


title: OX7464_6h_05


title: LS174T-Ethanol_16hours-rep1


title: HCT116-Calcitriol_16hours-rep1


title: HCT116-Ethanol_16hours-rep2


title: HOVON95: Newly diagnosed MM_207


title: sBPD, 33

description:
severe BPD
Sample name: 33


title: OX7464_6h_04


title: OX7464_6h_03


title: BPD+PH, 31

description:
BPD with Pulmonary Hypertension
Sample name: 31


title: BPD+PH, 28

description:
BPD with Pulmonary Hypertension
Sample name: 28


title: sBPD, 26

description:
severe BPD
Sample name: 26


title: sBPD, 24

description:
severe BPD
Sample name: 24


title: 231-CB-10uM-24hr-2

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

scan_protocol: Standard Illumina microarray protocol (BeadStudio)

data_processing: Expression values were normalized by quantile normalization method (R, LIMMA)

source_name: MDA-MB-231 cell-line

label_protocol: Total RNA were reverse transcribed, amplified by in vitro transcription and labelled with biotin-UTP using the Illumina Total Prep RNA amplification kit following the manufacturer's instructions. Labelled sample quality was assessed by spectrophotometry and bioanalyzer. After preheating at 65ºC for 5 min.

growth_protocol: 200,000 MDA-MB-231 cells per well were plated in 6-well plates with DMEM.

extract_protocol: RNeasy mini protocol (Qiagen Cat No./ID: 74104)

treatment_protocol: After 20-24 hours of incubation, cells were treated either with DMSO alone or with varying concentrations of  CB (5 and 10 μM) in DMSO for another 24 hours.

tag: cell type

value: breast cancer cell line

value: carbazole blue

tag: dose

tag: harvest


title: HOVON95: Newly diagnosed MM_206


title: HOVON95: Newly diagnosed MM_204


title: HOVON95: Newly diagnosed MM_205


title: OX7464_6h_01


title: 231-CB-5uM-24hr-2


title: HCT116-Ethanol_16hours-rep1


title: OX7417_6h_06

description:
OX7417_6h
oxstem_6h.csv
HL-60 cells treated with 1uM OXS007417 for 6h


title: BPD+PH, 23

description:
BPD with Pulmonary Hypertension
Sample name: 23


title: 231-CB-10uM-24hr-1


title: OX7417_6h_05


title: HOVON95: Newly diagnosed MM_202


title: 231-Control-24hr-2

value: vehicle


title: OX7417_6h_03


title: OX7417_6h_02


title: 231-CB-5uM-24hr-1


title: sBPD, 13

description:
severe BPD
Sample name: 13


title: sBPD, 12

description:
severe BPD
Sample name: 12


title: HOVON95: Newly diagnosed MM_203


title: OX7417_6h_01


title: HOVON95: Newly diagnosed MM_201


title: DMSO_6h_06

description:
DMSO_6h
oxstem_6h.csv
HL-60 cells treated with 0.1% DMSO for 6h

value: DMOS


title: sBPD, 11

description:
severe BPD
Sample name: 11


title: CPC_EV_2

description:
Sample 5
SV18531_0005_S23

value: cardiac progenitor cell


title: OX7464_6h_02


title: HOVON95: Newly diagnosed MM_200


title: 231-Control-24hr-1


title: BPD+PH, 6

description:
BPD with Pulmonary Hypertension
Sample name: 6


title: BPD+PH, 4

description:
BPD with Pulmonary Hypertension
Sample name: 4


title: HOVON95: Newly diagnosed MM_199


title: Plasmacytoid dendritic cells, oxLDL + CpG3

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

institute: Maastricht University

description:
DE30DIVLIAR100779
replicate 3

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Labeled cRNA was prepared and used on the Illumina HT12 v4.0 Beadchip array for hybridization. Hybridized chips were scanned by Illumina BeadStation.

data_processing: Raw image analysis and signal extraction was performed with Illumina Beadstudio Gene Expression software with default settings (no background subtraction) and no normalization.

label_protocol: CDNA was made from isolated RNA by reverse transcription using the iScript cDNA Synthesis Kit (Biorad). qRT-PCR was performed using SYBR Green PCR Master Mix (Biorad) as described previously40. IFN - delta-Ct expression is presented relative to beta-actin (housekeeping gene) expression.

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were prepared from heparinized whole blood of healthy donors by standard Ficoll-Paque density gradient centrifugation. PDCs were isolated from PBMCs using the BDCA-4 Cell Isolation Kit, or alternatively the pDC Diamond Kit. Labelled cells were enriched using permanent magnets yielding a high-gradient magnetic field. The positively sorted pDC fraction was analyzed by flow cytometry on a BD Canto II according to their BDCA-2+, CD123+, CD11c-, CD3-, CD14-, CD19-, CD20- and CD56- phenotype and reached > 90% purity.

extract_protocol: Total RNA was extracted from the cell suspensions using the RNeasy Micro kit, according to the manufacturer’s protocol for extraction of RNA from microdissected cryosections. DNA was removed by using 50U DNase I. RNA quantity and quality were determined using the NanoDrop-1000 Spectrophotometer and the Agilent’s 2100 Bioanalyzer System; average yield was 115 ng RNA and integrity numbers (RIN) were 6.5, reflecting limited half-life of human pDC in culture.

treatment_protocol: Isolated pDCs were seeded in round-bottomed 96-well cell culture plates at a density of 5x10e4 cells/ well in AIM-V medium, and cultured for 24 hours at 37°C and 5% CO2 in the presence of 2.5µM CpG-A, with or without LDL (50µg/ml) or oxLDL (10µg/ml or 50µg/ml) and plain medium supplemented with LDL (50µg/ml) or oxLDL (10µg/ml or 50µg/ml). In similar control experiments pDCs were stimulated by 5µg/ml imiquimod (IMI); 10 ng/ml lipopolysaccharide (LPS) or 10µg/ml of anti-CD40 antibody clone G.28.5, instead of CpG-A.

value: oxLDL + CpG

value: Blood

value: plasmacytoid dendritic cells


title: Plasmacytoid dendritic cells, oxLDL + CpG2

description:
DE57DIVLIAR100778
replicate 2


title: Plasmacytoid dendritic cells, oxLDL + CpG1

description:
DE84DIVLIAR100777
replicate 1


title: HOVON95: Newly diagnosed MM_195


title: HOVON95: Newly diagnosed MM_198


title: DMSO_6h_05


title: Plasmacytoid dendritic cells, oxLDL3

description:
DE14DIVLIAR100776
replicate 3

source_name: Plasmacytoid dendritic cells, oxLDL

value: oxLDL


title: HOVON95: Newly diagnosed MM_196


title: HOVON95: Newly diagnosed MM_197


title: Plasmacytoid dendritic cells, oxLDL2

description:
DE41DIVLIAR100775
replicate 2


title: Plasmacytoid dendritic cells, oxLDL1

description:
DE68DIVLIAR100774
replicate 1


title: BPD+PH, 7

description:
BPD with Pulmonary Hypertension
Sample name: 7

value: premature neonate

value: tracheal aspirate

value: no

value: yes


title: sBPD, 3

description:
severe BPD
Sample name: 3


title: DMSO_6h_04


title: DMSO_6h_03


title: HOVON95: Newly diagnosed MM_194

value: Male

value: bone marrow aspirate


title: ∆rv3143_3

city: Lodz

first: Przemyslaw

last: Plocinski

address: Lodowa 106

country: Poland

institute: Institute of Medical Biology of the Polish Academy of Sciences

data_processing:
unzipping the .gz file with gunzip function with Ubuntu Linux command line
seqencing adapter removal with Cutadapt software with parameters set cutadapt -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -g TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -G AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -A TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -q 15 && cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -g GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT -G TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -q 15
quality trimming was done with Sickle -pe script setting variable parameters as -t sanger -q 20 -l 20
mapping reads to the reference genome with Bowtie2 with default settings
sorting and indexing of the alignemnt files with Samtools
counting reads to features with HTSeq.count -t CDS -i Locus -m intersection-nonempty
count matrix was build in excel by merging the HTSeq.count output files
Genome_build: NC_000962.3 (H37Rv_v4.fasta)
Supplementary_files_format_and_content: DGE_Matrix.txt

organism: Mycobacterium tuberculosis H37Rv

source_name: bacteria grown in 7H9/10% OADC  medium

growth_protocol: The Mycobacterium tuberculosis H37Rv wild-type strain and ∆rv3143 mutant were grown in 7H9 broth (Becton-Dickinson) supplemented with 10% OADC enrichment (Becton-Dickinson). For RNA sequencing, the Mtb wild-type and ∆rv3143 mutant were grown to mid-logarythmic phase of growth. Bacteria were cultured in triplicate. 100 ml of each culture was spun down and subjected directly to total RNA isolation.

extract_protocol:
RNA was isolated using TRIzol LS reagent (Invitrogen). Cells were lysed by bead beating with the MP FastPrep system (MP Biomedicals) using lysing matrix B. DNA contamination of the RNA samples was removed by DNase I turbo (Invitrogen) digestion according to the manufacturer’s protocol. The quantity and integrity of the DNase I-treated RNA was assessed using an Agilent 2100 BioAnalyzer according to the manufacturer's instructions (Agilent RNA 6000 Nano Kit).
RNA samples were purified using AMPure XP magnetic beads (Becton Dickinson) with a 2.2:1 bead-to-RNA ratio. Two micrograms of the purified total RNA was used per library. The ribosomal RNA was removed with the Ribo-Zero Bacteria rRNA Removal Kit (Illumina) according to the manufacturer’s protocol. The Illumina-compatible RNA/cDNA sequencing libraries were prepared with the use of KAPA Stranded RNA-Seq kit (Roche) according to the detailed instructions provided by the manufacturer.

treatment_protocol: No treatment was applied. Wild type and mutant strain grown under the same conditions are compared.

tag: background strain

tag: genotype

value: Rv3143 mutant

tag: growth phase

value: grown to mid-exponential phase


title: DMSO_6h_02

tag: cell line


title: DMSO_6h_01


title: 0275_03

description:
0275_03
Oxstem_72h.csv
HL-60 cells treated with 1uM OXS000275 for 72h


title: ∆rv3143_1


title: hulled-less Pumpkins seed coat, 20 day after pollination, rep3 [HL_20_3]

city: HangZhou

first: Xiaolong

last: Lyu

address: No. 866, yuhangtang Road, Xihu Distric

country: China

institute: ZheJiang University

data_processing:
Transcriptome analysis was performed as described by Trapnell et al.
The clean reads filtered from raw data were mapped onto the Cucurbita pepo (Zucchini) Genome reference genome (http://cucurbitgenomics.org/organism/14). Low-quality reads (unknown nucleotides > 5% or low Q value ≤ 20%) were removed.
FPKM values were calculated to estimate gene expression levels by Cufﬂinks software. Differentially expressed genes were determined using the edgeR package of R software, and the false discovery rate ≤ 0.05 and the absolute value of log2 fold change ≥ 1 (|log2 FC|≥ 1) were used as the threshold to determine the statistically significant differences in gene expression.
Assembly: Cucurbita pepo
Supplementary files format and content: The excel file for the processed data

organism: Cucurbita pepo

source_name: seed coat

extract_protocol:
Total RNA was extracted from seed coats of hulled and hull-less pumpkins at 5 DAP, 10 DAP, and 20 DAP using a Trizol kit (Invitrogen, USA). Three biological replicates were performed for each stage.
1 µg RNA from each sample was taken for sequencing using an Illumina HiSeq 2000 platform.

value: seed coat

tag: sample group

value: hulled-less Pumpkins

tag: time point

value: 20 day after pollination


title: sBPD, 2

description:
severe BPD
Sample name: 2

tag: developmental stage


title: 0275_02

description:
0275_02
Oxstem_72h.csv
HL-60 cells treated with 1uM OXS000275 for 72h


title: wild_type_7H9_2

value: wild-type


title: BPD+PH, 1

description:
BPD with Pulmonary Hypertension
Sample name: 1

tag: tissue


title: hulled-less Pumpkins seed coat, 20 day after pollination, rep2 [HL_20_2]


title: 0275_01

description:
0275_01
Oxstem_72h.csv
HL-60 cells treated with 1uM OXS000275 for 72h


title: BPD+PH, 16

description:
BPD with Pulmonary Hypertension
Sample name: 16

tag: sbpd


title: DMSO_03

description:
DMSO_03
Oxstem_72h.csv
HL-60 cells treated with 0.1% DMSO for 72h

value: DMOS


title: hulled-less Pumpkins seed coat, 20 day after pollination, rep1 [HL_20_1]


title: OX7417_6h_04


title: wild_type_7H9_1


title: ∆rv3143_2


title: wild_type_7H9_3


title: hulled-less Pumpkins seed coat, 10 day after pollination, rep3 [HL_10_3]

value: 10 day after pollination


title: 3D Culture ctrl rep3

city: La Jolla

first: ZHENG

last: ZHONG

state: California

address: 9500 Gilman Dr

department: Nanoengineering

institute: University of California, San Diego

data_processing:
All the sequenced raw reads were filtered and trimmed with Trim Galore (version 0.4.1)
the clean reads were mapped to the human genome (grc38) using Hisat2
the number of reads uniquely mapped to each gene was determined using FeatureCount
Genome_build: grc38
Supplementary_files_format_and_content: reads count per gene

source_name: human conjunctival stem cells

growth_protocol: A customized DLP-based 3D bioprinting system was built with projection optics suppled with a 365 nm light source (Hamamatsu), a motion controller (Newport) and a digital micromirror device (DMD, Texas Instruments). The digital patterns were generated with MATLAB and inputted to the DMD chip through a custom-built coordination software. The thickness of the printed structures was controlled by the motion controller covered with polydimethylsiloxane (PDMS).  The bioprinted hydrogel structures were printed on methacrylated coverslips upon light exposure, then rinsed with warm DPBS before subjected to culture in 5% CO2 at 37℃.

extract_protocol:
Total RNA was purified using RNeasy per manufacturer’s instructions (Qiagen)
PolyA-tailed RNA was purified from total RNA and libraries were constructed using the NEBNext® Ultra™ II RNA Library Prep Kit (NEB) following manufacturer’s recommendations.

treatment_protocol: The pre-polymer solution for the printing was made by dissolving GelMA, HAGM and LAP with DPBS (ThermoFisher Scientific) and filtered with 0.22 μm syringe filter (Millipore Sigma). 5% or 8% (w/v) GelMA with 0.25% (w/v) LAP, and 2.5% (w/v) GelMA with 1% (w/v) HAGM and 0.25% (w/v) LAP were made accordingly. The 5% (w/v) GelMA was used as the soft condition for hCjSCs bioprinting while the 8% (w/v) GelMA was used as the stiff condition. 2.5% (w/v) GelMA with 1% (w/v) HAGM was used for the bioprinting of HUVECs and 10T1/2s. Before the printing, the cells were digested, filtered with 70 μm cell strainers (Corning), quantified for the cell concentration, and pelleted with desired quantity. For the hCjSCs bioprinting, the bioink contained 2×107 cells/mL of hCjSCs. For the multilayered printing of 3D pterygium model, the stem cell layer contained 2×107 cells/mL of hCjSCs plus 1×107 cells/mL of macrophages while the vascular layer contained 2×107 cells/mL of HUVECs and 4×105 cells/mL of 10T1/2s (50:1).

value: human conjunctival stem cells

tag: growth protocol

value: 3D Culture


title: HOVON95: Newly diagnosed MM_187

value: Female

value: multiple myeloma


title: 3D Culture ctrl rep2


title: hulled-less Pumpkins seed coat, 10 day after pollination, rep2 [HL_10_2]


title: HOVON95: Newly diagnosed MM_191


title: HOVON95: Newly diagnosed MM_192


title: HOVON95: Newly diagnosed MM_188


title: HOVON95: Newly diagnosed MM_186


title: Plasmacytoid dendritic cells, Ctrl2

description:
DE09DIVLIAR100769
replicate 2

source_name: Plasmacytoid dendritic cells, Ctrl

tag: treatment

value: Ctrl

value: Blood

value: plasmacytoid dendritic cells


title: hulled-less Pumpkins seed coat, 10 day after pollination, rep1 [HL_10_1]


title: PMA_03

description:
PMA_03
Oxstem_72h.csv
HL-60 cells treated with 10nM PMA for 72h

value: PMA


title: HOVON95: Newly diagnosed MM_190

tag: gender

value: bone marrow aspirate


title: 3D Culture ctrl rep1


title: Plasmacytoid dendritic cells, Ctrl1

description:
DE36DIVLIAR100768
replicate 1


title: Plasmacytoid dendritic cells, CpG2

description:
DE25DIVLIAR100772
replicate 2

source_name: Plasmacytoid dendritic cells, CpG

value: CpG


title: Plasmacytoid dendritic cells, Ctrl3

description:
DE79DIVLIAR100770
replicate 3


title: HOVON95: Newly diagnosed MM_189

value: Male

tag: age


title: Plasmacytoid dendritic cells, CpG3

description:
DE95DIVLIAR100773
replicate 3


title: HOVON95: Newly diagnosed MM_193

tag: disease state


title: Plasmacytoid dendritic cells, CpG1

description:
DE52DIVLIAR100771
replicate 1

tag: cell type


title: DMSO_02

description:
DMSO_02
Oxstem_72h.csv
HL-60 cells treated with 0.1% DMSO for 72h


title: PMA_02

description:
PMA_02
Oxstem_72h.csv
HL-60 cells treated with 10nM PMA for 72h


title: HOVON95: Newly diagnosed MM_185


title: Patient 123

first: Anton

middle: W.

last: Langerak

address: Doctor Molewaterplein 40

description: IGH gene repertoire sequencing from pre-diagnostic CLL patients and controls

library_source: genomic

data_processing:
Library strategy: B-cell receptor repertoire
Raw FASTQ files were uploaded to the ARResT/Interrogate immunoprofiler for annotation and initial exploratory analysis. The full productive IGH repertoire for each sample was downloaded in .csv format and processed in R (R Core Team, 2020) during further analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited tekst file containing: sample,QC.status,scenario,rearrangements,raw.count,w.junction.count,w.junction.percent,artefacts.count,artefacts.percent,usable.count,usable.percent,w.most.pop.cln.s..count,w.most.pop.cln.s..percent,uniq.usable.seq.count,clonotypes.count,diversity..norm.ed..count,effective.species.count,R1.Q.mean.stdev.count,R2.Q.mean.stdev.count,joined.normally.count,joined.normally.percent,joined.loosely.count,joined.loosely.percent,total.joined.count,total.joined.percent,saved.from.unjoined.count,saved.from.unjoined.percent,low.quality..ee.nt...0.01..count,low.quality..ee.nt...0.01..percent,short...50nt..count,short...50nt..percent,annotated.count,annotated.percent,w.TR.receptor.count,w.TR.receptor.percent,w.B.chain.count,w.B.chain.percent,w.VJ.Vb..Db..Jb.count,w.VJ.Vb..Db..Jb.percent,w.VJ.Vb..Db..Jb.cln

molecule: genomic DNA

source_name: Buffy coat

growth_protocol: Blood  samples were collected at from healthy volunteers, buffycoats and serum were stored at -80 °C until further analysis

extract_protocol:
Total  gDNA was isolated from the buffycoat DNA and 250-500 ng was amplified through multiplex PCR of IGHV-IGHD-IGHJ gene rearrangements following the BIOMED-2 protocol. After amplification, PCR products were purified on Agencourt AMPURE beads (Beckman Coulter, Brea, CA, USA) and eluted using H2O. The purified product was checked for primer dimers using the Agilent Tapestation (Agilent,Santa Clara, CA, USA).
The intitial multiplex PCR already attached the indexes to the PCR products, so library construction was simply pooling the purified PCR product in equilmolar fashion.

value: leukocytes

tag: diagnosis

value: CLL

tag: sample type

value: Pre-diagnostic


title: hulled-less Pumpkins seed coat, 5 day after pollination, rep2 [HL_5_2]

value: seed coat

value: hulled-less Pumpkins

value: 5 day after pollination


title: Patient 124


title: hulled-less Pumpkins seed coat, 5 day after pollination, rep3 [HL_5_3]


title: PMA_01

description:
PMA_01
Oxstem_72h.csv
HL-60 cells treated with 10nM PMA for 72h


title: hulled-less Pumpkins seed coat, 5 day after pollination, rep1 [HL_5_1]


title: Patient 122


title: APEX-seq APEX2DDX3Y_wArs_rep2

city: philadelphia

first: Fange

last: Liu

state: PA

address: 415 curie blvd, Clinical Research Building Rm 350

institute: UPENN

data_processing:
The high throughput sequencing reads were adaptor and quality trimmed using Trimmomatic with following command: trimmomatc SE -phred33 ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:25 TRAILING:25 SLIDINGWINDOW:4:20 MINLEN:30.
Then, the reads were aligned to the GRCh38 human genome reference using HISAT2. Parameters used were: --no-unal (not report the unaligned reads), --known-splicesite-file (generated from the Ensembl hg38 annotation file) and –k 1 (report one alignment).
Aligned reads were quantified using featureCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: APEX-seq APEX2DDX3Y_wArs

growth_protocol: HeLa cells were cultured in DMEM + GlutaMAX (GIBCO, 11995065) with 10% FBS (GIBCO, 26140-079) and 1% Pen/Strep (Corning, 30-002-CI) in a humidified incubator with 5% CO2¬ at 37°C.

extract_protocol:
After the cellular labeling, total RNA was purified using TRIzol per the manufacturer’s instruction. To enrich biotinylated RNAs, Pierce streptavidin magnetic beads (Thermo Fisher) were used (20 μL beads per 50 μg RNA). The beads were washed 3 times with 500 μL B&W buffer (5 mM Tris-HCl, pH 7.5, 0.5 mM EDTA, 1 M NaCl, and 0.1% TWEEN 20), followed by 2 times of 500 μL solution A (0.1 M NaOH and 50 mM NaCl), and 1 time of 500 μL solution B (100 mM NaCl). The beads were then suspended in 125 μL solution B. 50 μg RNA diluted in 125 μL water was mixed with the beads and incubated at 4 °C for 2 hrs with rotation. Then, the beads were placed on a magnetic stand to remove the solution and washed 3 times with 500 μL B&W buffer. Finally, the beads were resuspended in 54 μL water. To release the biotinylated RNA, 33 μL proteinase buffer (3 x PBS, 6% N-Lauryl sarcosine sodium solution (Sigma-Aldrich), 30 μM EDTA, and 15 μM DTT) was added to the beads with 10 μL proteinase K (Thermo Fisher) and 5 μL RNase inhibitor. The beads were then incubated at 42 °C for 1 hr and 55 °C for 1 hr on a shaker at 600 rpm. The RNA was then purified using the RNA clean and concentrator 5 kit (Zymo Research) following the manufacturer’s instruction. The resulted RNA was then used for RNA-seq library construction.
Libraries were constructed according to TruSeq Stranded mRNA Kit (Illumina) protocol. The concentrations for all the libraries were determined by KAPA Library Quantification Kit (KAPA Biosystems) following the manufacturer’s protocol, and subjected to Next-generation high-throughput sequewncing using an illumina NextSeq 550 with a single-end 75-bp read length.

treatment_protocol: To enable APEX labeling in mammalian cells, prewarmed 5 mL of biotin-phenol (at 500 mM final concentration)-containing DMEM media was added to the cells for 30 minutes prior to the start of the experiment. To label the stressed cells, media containing 500 μM sodium arsenite was used to treat cells for 30 min, and prewarmed 5mL DMEM media containing 500 mM biotin-phenol and 500 μM sodium arsenite was used to treat for another 30 min. H2O2 (Sigma-Aldrich) was added to each dish at 1 mM final concentration for a total labeling time of exactly 1 minute with gentle agitation. To stop labeling after 1 min treatment, the culture media was removed, and the quenching solution (10 mM sodium ascorbate, 10 mM sodium azide, and 5 mM Trolox in PBS) was immediately used to wash the cells for three times.  Finally, 1 mL quenching solution was applied to cover the cells. Cells were then collected with cell scraper.

value: HeLa

tag: genotype/variation

value: APEX2-DDX3Y stable expression

value: 500 mM Sodium Arsenite for 1 hr


title: hulled Pumpkins seed coat, 20 day after pollination, rep3 [H_20_3]

value: hulled Pumpkins

value: 20 day after pollination


title: HOVON95: Newly diagnosed MM_184

value: multiple myeloma


title: APEX-seq APEX2DDX3Y_wArs_rep1


title: hulled Pumpkins seed coat, 20 day after pollination, rep2 [H_20_2]


title: HOVON95: Newly diagnosed MM_183

value: Female


title: Patient 120


title: Patient 119


title: HOVON95: Newly diagnosed MM_180


title: HOVON95: Newly diagnosed MM_181


title: APEX-seq APEX2DDX3X_wArs_rep1

source_name: APEX-seq APEX2DDX3X_wArs

value: APEX2-DDX3X stable expression


title: hulled Pumpkins seed coat, 10 day after pollination, rep3 [H_10_3]

value: 10 day after pollination


title: Patient 118


title: APEX-seq APEX2EGFP_wArs_rep2

source_name: APEX-seq APEX2EGFP_wArs

value: APEX2-EGFP stable expression


title: hulled Pumpkins seed coat, 10 day after pollination, rep2 [H_10_2]


title: Patient 117


title: APEX-seq APEX2EGFP_wArs_rep1


title: hulled Pumpkins seed coat, 10 day after pollination, rep1 [H_10_1]


title: SG231_monolayer_2

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

data_processing:
base calling with bcl2fastq 2.20.0.422
read cleaning with fastp (v0.20.0): fastp -A -q 30 -u 50 -l 70 -y -w 20 -i raw/r1_raw -I raw/r2_raw -o pre/r1_prep -O pre/r2_prep -h pre/log.html -j /dev/null
read mapping with salmon (v0.14.1): salmon quant -p 22 --numGibbsSamples 500 -i genome -l A -1 r1_prep -2 r2_prep --validateMappings -o mapped
data collection: R (v3.6.3) Bioconductor tximport (v1.14.2)
analysis package: R Bioconductor DESeq2 (v2_1.26.0)
Genome_build: Homo sapiens GRCh38.p13
Supplementary_files_format_and_content: transcript and gene abundance tables both as R saved file and tab-separated txt file

source_name: SG231 cell line

growth_protocol: The cells were grown for 10 days in anchoring-independent conditions with selective serum-free Dulbecco’s modified Eagle’s medium (DMEM)/F12 medium supplemented with 1X B27 supplement minus vitamin A , human recombinant epidermal growth factor (hrEGF) (20 ng/ml), and bFGF (20 ng/ml).

extract_protocol:
Total RNA was isolated from cells using the miRNeasy Mini Kit (Qiagen) according to the manufacturer's protocol. Depletion of mammalian and mitochondrial rRNA was performed with the RiboGone – Mammalian kit according to manufacturer's instructions
Paired-end RNA libraries were prepared for sequencing using standard Illumina protocols

value: cholangiocarcinoma

tag: growth type

value: monolayer

tag: replicate


title: Patient 116

value: leukocytes

value: CLL


title: HOVON95: Newly diagnosed MM_178

value: Male

value: bone marrow aspirate


title: hulled Pumpkins seed coat, 5 day after pollination, rep3 [H_5_3]

value: seed coat

value: 5 day after pollination


title: hulled Pumpkins seed coat, 20 day after pollination, rep1 [H_20_1]


title: Patient 115

value: Pre-diagnostic


title: HOVON95: Newly diagnosed MM_177


title: HOVON95: Newly diagnosed MM_174


title: hulled Pumpkins seed coat, 5 day after pollination, rep2 [H_5_2]


title: HOVON95: Newly diagnosed MM_176


title: HOVON95: Newly diagnosed MM_179


title: HOVON95: Newly diagnosed MM_175


title: SG231_spheroid_2

tag: cell line

value: spheroid


title: Patient 114


title: hulled Pumpkins seed coat, 5 day after pollination, rep1 [H_5_1]

tag: sample group

value: hulled Pumpkins


title: HOVON95: Newly diagnosed MM_182


title: Patient 113


title: CCLP1_spheroid_2

source_name: CCLP1 cell line


title: Patient 112


title: Non-muscle invasive bladder cancer 31-post [D378R084]

city: Singapore

first: Tuan Zea

last: Tan

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

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description: post-treatment  31

data_processing:
bcl2fastq 2.17.1.14 were used for basecalling.
Sequenced reads were mapped to hg19 using STAR v2.4.2a with default parameters settings
Counts Per Kilobase per Megabase of library size (CPM) were computed using RSEM v1.2.25 and Gencode v35 annotation.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include CPM values for every gene of Sample

source_name: FFPE

extract_protocol:
RNA from the FFPE sections were extracted using QIAGEN Rneasy FFPE kit.
RNA libraries were prepared for sequencing using QUANTSEQ 3’mRNA-Seq Library Prep (REV) LEXOGEN kit & standard Illumina protocol.

value: Bladder

value: Post-treatment

tag: case


title: Non-muscle invasive bladder cancer 22-recur [D378R083]

description: recurrent 22

value: Recurrent tumor


title: HOVON95: Newly diagnosed MM_173

value: multiple myeloma


title: HOVON95: Newly diagnosed MM_172


title: NHC3_monolayer_3

source_name: NHC3 cell line


title: SG231_spheroid_3


title: APEX-seq APEX2DDX3X_wArs_rep2

value: HeLa

value: APEX2-DDX3X stable expression

value: 500 mM Sodium Arsenite for 1 hr


title: DMSO_01

description:
DMSO_01
Oxstem_72h.csv
HL-60 cells treated with 0.1% DMSO for 72h

source_name: HL60 cell line

value: DMOS


title: Patient 121

value: leukocytes


title: Patient 110

value: CLL


title: Non-muscle invasive bladder cancer 12-recur-2 [D378R082]

description: recurrent 12


title: HOVON95: Newly diagnosed MM_171

source_name: bone marrow aspirate

value: Female


title: Patient 109


title: Non-muscle invasive bladder cancer 33 [D378R079]

description: Primary tumor 33

value: Primary tumor


title: Patient 111


title: SG231_spheroid_1

value: cholangiocarcinoma


title: CCLP1_monolayer_2

value: monolayer


title: CCLP1_monolayer_3


title: HUCCT1_monolayer_3

source_name: HUCCT1 cell line


title: Non-muscle invasive bladder cancer 27-recur-2 [D378R080]

description: recurrent 27


title: Non-muscle invasive bladder cancer 27 [D378R030]

description: Primary tumor 27


title: Non-muscle invasive bladder cancer 14-recur [D378R081]

description: recurrent 14


title: Patient 107

value: Pre-diagnostic


title: HOVON95: Newly diagnosed MM_169

value: Male

value: bone marrow aspirate


title: HOVON95: Newly diagnosed MM_170


title: Patient 104


title: Non-muscle invasive bladder cancer 12 [D378R033]

description: Primary tumor 12

value: Bladder


title: NHC3_monolayer_1


title: HUCCT1_spheroid_3

value: spheroid


title: HOVON95: Newly diagnosed MM_164


title: Patient 108


title: SG231_monolayer_1


title: HOVON95: Newly diagnosed MM_166


title: Patient 105


title: HOVON95: Newly diagnosed MM_167


title: HUCCT1_monolayer_2


title: Patient 102


title: Non-muscle invasive bladder cancer 22 [D378R025]

description: Primary tumor 22


title: HOVON95: Newly diagnosed MM_168


title: Patient 106


title: NHC3_monolayer_2


title: HOVON95: Newly diagnosed MM_161


title: Non-muscle invasive bladder cancer 25 [D378R022]

description: Primary tumor 25


title: HOVON95: Newly diagnosed MM_163


title: Non-muscle invasive bladder cancer 26 [D378R015]

description: Primary tumor 26


title: Patient 103


title: Patient 101


title: CCLP1_monolayer_1


title: HUCCT1_monolayer_1


title: CCLP1_spheroid_1


title: Patient 99


title: HOVON95: Newly diagnosed MM_162


title: MTCHC01_monolayer_2

source_name: MTCHC01 cell line


title: hsDG99HC_HHT

city: New Haven

first: Le

last: Zhang

state: CT

address: 300 George Street

department: Neurology

institute: Yale University

description:
Single nucleus RNA sequencing
Brain nuclei
Nuclear RNA

library_source: transcriptomic single cell

data_processing:
A custom pre-mRNA human genome reference was generated with GRCh38 (Ensembl 93) that included pre-mRNA sequences by 10x Cell Ranger.
snRNA-seq data were aligned to this GRCh38–premRNA human genome reference (Ensembl 93) to map both unspliced pre-mRNA and mature mRNA using 10x CellRanger version 3.1.0.
Assembly: GRCh38 (Ensembl 93), GRCh38-premRNA
Supplementary files format and content: Filtered gene expression matrix. Barcodes.tsv, genes.tsv, matrix.mtx.

source_name: brain

extract_protocol:
Nuclei were isolated from post-mortem fresh frozen human brain tissue. Frozen tissue (50 to 100 mg) was homogenized in 15 ml of ice-cold nuclei homogenization buffer [2 M sucrose, 10 mM Hepes (pH 7.9), 25 mM KCl, 1 mM EDTA (pH 8.0), 10% glycerol, and ribonuclease (RNase) inhibitors freshly added (80 U/ml)] with Dounce tissue grinder (10 strokes with loose pestle and 10 strokes with tight pestle). The homogenate was transferred into an ultracentrifuge tube on top of 10 ml of fresh nuclei homogenization buffer and centrifuged at 25,000 rpm for 60 min at 4°C on a ultracentrifuge. The supernatant was removed, and the pellet was resuspended in 1 ml of nuclei resuspension buffer [15 mM Hepes (pH 7.4), 15 mM NaCl, 60 mM KCl, 2 mM MgCl2, 3 mM CaCl2, and RNase inhibitors freshly added (80 U/ml)] and counted on a hemocytometer for 10x loading.
The snRNA-seq libraries were prepared by the 10x Genomics Chromium Single Cell 3′ Reagent Kit v3 chemistry according to the manufacturer’s instructions and sequenced using Illumina NovaSeq6000 S4.
Single nucleus RNA sequencing, 10x Genomics Chromium Single Cell 3′ Reagent Kit v3.

value: Control

value: prefrontal cortex

tag: cellular fraction

value: nuclei

tag: time point

value: postmortem


title: HOVON95: Newly diagnosed MM_159

tag: tissue

value: multiple myeloma


title: HOVON95: Newly diagnosed MM_165


title: Patient 100


title: Patient 98


title: hsDG197PD_HHT

value: Parkinson's disease


title: HOVON95: Newly diagnosed MM_157


title: HSDG199PD_HHT


title: Patient 97

value: leukocytes


title: hsDG151PD_HHT


title: HOVON95: Newly diagnosed MM_158


title: hsDG30HC_HHT


title: hsDG208PD_HHT


title: HOVON95: Newly diagnosed MM_160


title: Patient 95

value: CLL


title: HSDG148PD_HHT


title: hsDG142PD_HHT


title: Patient 93


title: Patient 94


title: hsDG13HC_HHT


title: HOVON95: Newly diagnosed MM_155


title: HSDG10HC_HHT


title: HOVON95: Newly diagnosed MM_156


title: HOVON95: Newly diagnosed MM_153


title: Patient 92


title: Patient 91


title: hsDG101HC_HHT


title: Plasma-Ctrl-rep2

city: Beijing

first: Jinghua

last: Yang

address: 32 North Third Ring Road West, Haidian District, Beijing

institute: Beijing Zhiyun data technology co. LTD

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at The Agilent Feature Extraction Software (version 11.0.1.1) was used to analyze and extract array images. Quantile normalization and subsequent data processing were conducted in GeneSpring GX v12.1 software package (Agilent Technologies). Threshold defined as fold-change > 2.0 (Student’s t test, P < 0.05) was used as a volcano plot filtering for DE lncRNAs and mRNAs.

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Frozen plasma from BBR and Ctrl group were cryo pulverized using biopulverizer (Biospec) and homogenized with TRIzol (Invitrogen Life Technologies) by Mini-Bead-Beater-16 (Biospec). RNA was collected from each sample based on the manufacturer’s protocols.

treatment_protocol: Whole blood was collected using an EDTA anticoagulation tube and plasma was separated as soon as possible: 1000g centrifugation for 10 minutes to separate plasma and cellular components.The collected plasma was transferred to individual anticoagulation tubes and dispensed at 300-500 ul/tube. The dispensed plasma were perserved at -80℃.

value: Plasma


title: HOVON95: Newly diagnosed MM_151


title: Plasma-Ctrl-rep5


title: HOVON95: Newly diagnosed MM_154

value: Female


title: Plasma-Ctrl-rep4


title: Plasma-BBR-rep5

value: Berberine


title: Plasma-Ctrl-rep3


title: Patient 90


title: Patient 89


title: Plasma-Ctrl-rep1


title: inVitro_D370_pos_brep2

city: Dresden

first: Marius

last: Ader

address: Fetscherstrasse 105

department: Center for Regenerative Therapies Dresden

country: Germany

institute: TU Dresden

data_processing:
basecalling:
Basecalls were done with Illumina bcl2fastq version 2.19.1 (Illumina NextSeq 500 files) and 2.20.0 (Illumina NovaSeq 6000 files).
xenograft filtering:
A xengsort (v2021-05-27) index based on human and mouse genome and transcript sequences obtained form Ensembl92 was built (parameter:  -k 25  -n 4496607845 --type 3FCVbb --unaligned  --hashfunctions linear945:linear9123641:linear349341847  -p 4 --fill 0.88 -T 1 --shortcutbits 0). Mouse reads were identified with xengsort (parameter: --threads 20 --chunksize 16.0 --prefetch 1) and removed, that is, only reads uniquely assigned to human were kept.
mapping:
Xenograft-filtered reads were aligned to the human reference genome hg38 using the aligner gsnap (v2020-12-16) with Ensembl 92 human splice sites as support (parameter: --gunzip -A sam -t 11 --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -n 1 -m 0.6 -s EnsemblGene-92.ss.hg38.iit -N 0 --read-group-id=L62689_H6x6C52Lc --read-group-name=H6x6C52Lc --read-group-library=L62689 --read-group-platform=illumina --action-if-cigar-error noprint fastq/L62689_H6x6C52Lc_R1.fastq.gz fastq/L62689_H6x6C52Lc_R2.fastq.gz).
counts per feature:
Uniquely mapped reads were compared based on their overlap to Ensembl 92 human gene annotations using featureCounts (v2.0.1) to create a table of fragments per human gene and sample (parameter: featureCounts -a EnsemblGene-92.hg38.TR.gtf -s 0 -p -o bfx1362.hg38.e92.txt -Q 1 -T 8).
Assembly: hg38
Supplementary files format and content: bfx1362.hg38.e92.txt.gz is a tab-separated file with the output from FeatureCounts. Each row represents a gene and the columns contain the gene information followed by the sample counts.

source_name: in vitro generated human retinal organoids

growth_protocol: Detailed description of the human retinal organoid generation protocol can be found in the supplementary methods of the manuscript.

extract_protocol:
Detailed description of retrieval and sorting of human cells from murine eyecups as well as dissociation and sorting of cells from human retinal organoids in vitro can be found in the methods section of the manuscript.
RNAseq was based on Smart-seq2 sensitive full-length transcriptome profiling and modified from Picelli et. al., 2013 (Picelli et al., 2013).

treatment_protocol: Detailed description of the transplantation procedure can be found in the methods of the manuscript.

tag: alternative name

value: mCar-GFP in PGP1 human iPSC

tag: origin

value: inVitro

tag: total age_in_days

tag: fraction

value: pos

tag: dissociation protocol

value: Retinal organoids were dissociated as described in the methods of the manuscript, filtered and sorted directly into lysis buffer.


title: Patient 88

tag: cell type

value: Pre-diagnostic


title: inVitro_D370_pos_brep1

value: in vitro generated human retinal organoids


title: HOVON95: Newly diagnosed MM_150

tag: gender

value: Male

tag: age

value: bone marrow aspirate

tag: disease state


title: Patient 87

tag: diagnosis

tag: sample type


title: inVitro_D370_neg_brep3

tag: cell line

value: neg


title: Patient 86


title: inVitro_D370_neg_brep2


title: Patient 85


title: inVitro_D370_neg_brep1


title: Patient 84


title: Patient 83


title: Patient 82


title: 8-CA-CYS4-Re

city: Jinan

first: Wenqiang

last: Chang

state: Shandong

address: No. 44 West Wenhua Road

institute: Shandong University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Candida albicans

source_name: Candida albicans

growth_protocol: Overnight grown C. albicans CAF2-1, cys4Δ/Δ, cys4Δ/Δ+CYS4 cells were diluted to 1E6 cells per milliliter using RPMI1640 medium and cultured for 5 h at 37 ℃.

extract_protocol:
RNA was extracted using a RiboPure-Yeast kit (Ambion) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strains

value: Candida albicans CYS4 integrated strain

tag: genotype

value: cys4::hisG/ cys4::hisG ura3::imm434/ura3::imm434 RPS1/ RPS1::PMET3-CYS4-URA3


title: 9-CA-CYS4-Re

treatment_protocol: Overnight grown C. albicans CAF2-1, cys4Δ/Δ, cys4Δ/Δ+CYS4 cells were diluted to 1E6 cells per milliliter using RPMI1640 medium and cultured for 5 h at 37 ℃.


title: 6-CA-cys4-d

value: Candida albicans cys4 mutant


title: 7-CA-CYS4-Re


title: 5-CA-cys4-d


title: exVivo_D200_26w_pos_brep3

value: exVivo

tag: age donor_cells

tag: time in_vivo

value: Whole murine eye cups containing transplanted human cones were dissociated with papain as described in the methods section of the manuscript, filtered and sorted directly into lysis buffer.


title: exVivo_D200_26w_pos_brep1_trep3

tag: tissue


title: exVivo_D200_26w_pos_brep2

tag: alternative name


title: HOVON95: Newly diagnosed MM_149

value: multiple myeloma


title: Patient 81

value: leukocytes

value: CLL


title: exVivo_D200_26w_pos_brep1_trep2

value: mCar-GFP in PGP1 human iPSC

tag: origin


title: Plasma-BBR-rep4

value: Plasma

tag: treatment

value: Berberine


title: Patient 80


title: 3-CA-wt

value: Candida albicans CAF2-1


title: 4-CA-cys4-d


title: 2-CA-wt


title: 1-CA-wt


title: exVivo_D200_26w_pos_brep1_trep1

tag: total age_in_days

tag: fraction

value: pos


title: HOVON95: Newly diagnosed MM_139


title: HOVON95: Newly diagnosed MM_141

value: Female


title: HOVON95: Newly diagnosed MM_143

value: Male


title: HOVON95: Newly diagnosed MM_142

value: bone marrow aspirate


title: HOVON95: Newly diagnosed MM_144


title: HOVON95: Newly diagnosed MM_146


title: Plasma-BBR-rep3


title: HOVON95: Newly diagnosed MM_148


title: Plasma-BBR-rep2


title: HOVON95: Newly diagnosed MM_147


title: Patient 79

tag: cell type

value: Pre-diagnostic


title: Patient 78


title: HOVON95: Newly diagnosed MM_140

tag: gender


title: Huh7, Sph, rep3

city: Guangzhou

first: Peng

last: Ye

state: Guangdong Province

address: Xinzao, Panyu District, Guangzhou, P.R.China

department: center for cancer and immunology research

institute: Guangzhou Medical University

data_processing:
Illumina Casava2.19 software used for basecalling
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes FPKM values  for every gene and every sample

source_name: Huh7 cells

extract_protocol:
TRIZOLreagent was used to collect total RNA from cells. RNA degradation and contamination was monitored on 1% agarose gels. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: hepatocelluar carcinoma cell

tag: growth protocol

value: Spheroid culture


title: HOVON95: Newly diagnosed MM_145

tag: age

tag: disease state


title: Patient 77

tag: diagnosis

tag: sample type


title: HOVON95: Newly diagnosed MM_152


title: Patient 96


title: Huh7, Sph, rep2

tag: cell line


title: HOVON95: Newly diagnosed MM_137


title: Patient 76


title: Huh7, Adh, rep3

value: Adherent culture


title: HOVON95: Newly diagnosed MM_138


title: HSDG07HC_HHT

value: Control

value: prefrontal cortex

tag: cellular fraction

value: nuclei

tag: time point

value: postmortem


title: Huh7, Adh, rep2


title: Patient 75

value: leukocytes

value: CLL


title: Patient 74


title: NASH_Liver_6w_rep2

city: Hirosaki

first: Mitsuru

last: Chiba

state: Aomori

address: 66-1 Hon-cho

department: Graduate School of Health Sciences

country: Japan

institute: Hirosaki University

description: Gene expression at 6 week after a high-fat diet intake

hyb_protocol: 600 ng of Cy3-labeled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 uL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 uL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE microarray 8x60K ver. 2.0 (G4852A) (Agilent Technologies) for 17 hours at 65°C in a rotating hybridization oven (Agilent Technologies).  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G4900DA) (Agilent Technologies) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 2 um high sensitivity, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent Technologies) using default parameters (protocol GE1_1105_Oct12 and Grid: 028005_D_F_20171030) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Data obtained were processed using GeneSpring GX14.5 software (Agilent Technologies) to normalize all values to 75% percentile shift on the respective microarrays, followed by the normalization of the median expression level of all samples. In addition, the minimum expression value was set at 50 to filter by expression level. GeneSpring GX14.5 software was used to obtain expression data with more than 1.5-fold expression change in the NASH group compared to the Control group. Matrices were denoted with normalized gProcessedSignal.

organism: Mus musculus

source_name: NASH Liver, 6 weeks, replicate 2

label_protocol: Cy3-labeled cRNA was synthesized from 150 ng of liver total RNA using a Low Input Quick Amp Labeling Kit (Agilent Technologies), according to the manufacturer’s instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNAs from livers were extracted using the Isogen II reagent (Nippon gene), according to the manufacturer’s instructions. The quality and concentration of total RNAs were assessed using a NanoDrop spectrophotometer (NanoDrop Technologies). All RNA samples had 260/280 nm absorbance ratios of 1.8–2.0. The peaks of total RNAs were confirmed using an Agilent 2100 Bioanalyzer and an Agilent RNA 6000 Pico Kit (Agilent Technologies), according to the manufacturer’s instructions.

treatment_protocol: Five-week-old C57BL/6NJcl male mice were purchased from Clea Japan and acclimatized for 1 week before starting the experiment. For up to 6 weeks, the mice were fed a choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD, A06071302, RESEARCH DIETS) consisting of 60 kcal% fat and 0.1% methionine by weight to induce the onset of NASH. A dietary breeding solid-type feed CE-2 (Clea Japan) was fed to a control mouse group under the same conditions other than the diet. A sampling in each control and NASH group was performed at 1, 2, and 6 weeks.

value: liver

value: male

tag: diet

value: high-fat


title: Huh7, Sph, rep1


title: Patient 73

source_name: Buffy coat


title: Huh7, Adh, rep1


title: ActD_12 Hr _iN_SNCA_4COPY_PFF added_Replicate3

city: Boston

first: Xianjun

last: Dong

state: MA

address: 60 Fenwood Rd

institute: Brigham and Women's Hospital

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using star v2.7.1a with parameters --runMode alignReads \        --twopassMode Basic \        --readFilesCommand zcat \        --outSAMtype BAM SortedByCoordinate \        --outFilterType BySJout \        --outFilterMultimapNmax 100 \        --outFilterMismatchNmax 999 \        --outFilterMismatchNoverLmax 0.1 \        --alignIntronMax 1000000 \        --alignMatesGapMax 1000000 \        --alignSJoverhangMin 8 \        --alignSJDBoverhangMin 1 \        --chimOutType Junctions \        --chimSegmentMin 10 \        --chimJunctionOverhangMin 15 \        --runThreadN 4 \        --outSAMstrandField intronMotif \        --outSAMunmapped Within
Raw reads counts were calculated using htseq-count (0.6.1) with parameters -m intersection-strict -t exon -i gene_id -s no -q -f bam accepted_hits.bam and gencode.v37 as GTF.
Assembly: hg38
Supplementary files format and content: tab-delimited text file for raw counts of sequencing reads for ENSEML genes in all samples

source_name: Patient derived Ngn2 induced cortical neurons

growth_protocol: Please see Hallacli et.al.,2022,CELL

extract_protocol:
Trizol based total RNA extraction with the kit (PureLink™ RNA Mini Kit, Thermo Fisher)
KAPA mRNA HyperPrep Kit with oligo dT capture

treatment_protocol: ActinomycinD(10 ug/ml final), SNCA preformed fibril(5 ug/ml final)

tag: snca genotype

value: Parkinson's Disease model

tag: pff treatment

value: PFFyes

tag: timepoint


title: HOVON95: Newly diagnosed MM_136

first: Mark

last: van Duin

address: Wytemaweg 80

data_processing: MAS5.0 (Bioconductor affy package v1.36.2) default values with a trimmed mean target intensity value set to 1500. Values below 30 were truncated.

extract_protocol: RNeasy

value: Female

tag: tissue

value: multiple myeloma


title: Patient 72

value: Pre-diagnostic


title: HOVON95: Newly diagnosed MM_135

value: Male

value: bone marrow aspirate


title: Control_Liver_6w_rep2

description: Gene expression at 6 week after a control diet intake

source_name: Control Liver, 6 weeks, replicate 2

value: control


title: NASH_Liver_2w_rep2

description: Gene expression at 2 week after a high-fat diet intake

source_name: NASH Liver, 2 weeks, replicate 2


title: Control_Liver_6w_rep1

source_name: Control Liver, 6 weeks, replicate 1


title: NASH_Liver_6w_rep1

source_name: NASH Liver, 6 weeks, replicate 1


title: HOVON95: Newly diagnosed MM_132


title: ActD_12 Hr _iN_SNCA_4COPY_PFF added_Replicate1

value: Patient derived Ngn2 induced cortical neurons


title: inVitro_D370_pos_brep3

tag: alternative name

value: in vitro generated human retinal organoids

value: mCar-GFP in PGP1 human iPSC

tag: origin

value: inVitro

tag: total age_in_days

value: pos

tag: dissociation protocol

value: Retinal organoids were dissociated as described in the methods of the manuscript, filtered and sorted directly into lysis buffer.


title: NASH_Liver_2w_rep1

source_name: NASH Liver, 2 weeks, replicate 1

value: liver

tag: gender


title: ActD_12 Hr _iN_SNCA_4COPY_PFF added_Replicate2

tag: cell type


title: Patient 70

value: leukocytes

value: CLL


title: Patient 71


title: HOVON95: Newly diagnosed MM_133

tag: age

tag: disease state


title: Patient 69

tag: diagnosis

tag: sample type


title: Plasma-BBR-rep1

value: Plasma

tag: treatment

value: Berberine


title: Control_Liver_2w_rep2

description: Gene expression at 2 week after a control diet intake

source_name: Control Liver, 2 weeks, replicate 2

value: male


title: Patient 68


title: HOVON95: Newly diagnosed MM_130

value: Female

value: multiple myeloma


title: ActD_12 Hr _iN_SNCA_4COPY_No PFF_Replicate3

value: Parkinson's Disease model

value: PFFno


title: HOVON95: Newly diagnosed MM_134

value: Male

value: bone marrow aspirate


title: ActD_12 Hr _iN_SNCA_4COPY_No PFF_Replicate2

value: Patient derived Ngn2 induced cortical neurons


title: ActD_12 Hr _iN_SNCA_4COPY_No PFF_Replicate1


title: Patient 67

value: Pre-diagnostic


title: HOVON95: Newly diagnosed MM_127


title: Toropolone rep2

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

country: South Korea

institute: Pusan National University

data_processing:
Using FASTX-Toolkit, raw data derived from RNA-seq was filtered to a minimum phred quality score of 28.
The BWA-MEM algorithm was employed to align the filtered reads into the reference genome.
SAM files were converted to BAM files of binary format, and then sorted by chromosomal coordinates using the SAMtools program.
Mapped reads per annotated gene were counted by featureCounts tool in the Subread package.
Counted values were nomalised in the RPKM method.
Genome_build: Escherichia coli K-12 MG1655 GCF_000005845.2
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each Sample

organism: Escherichia coli

source_name: Bacterial culture with 100 uM tropolone

growth_protocol: E. coli K-12 MG1655 was incubated in 3 ml LB liquid for 14 h at 37℃ with constant shaking, and then 10 uM toxoflavin and 100 uM tropolone dissolved in methanol were added to each culture. Additional incubation was performed for 2 h.

extract_protocol:
After 2 h of the treatment, 1 ml of each culture centrifuged and total RNA was prepared using RNeasy Midi kit (Qiagen, Valencia, CA, USA) according to the manufacturer's protocols. A MICOBExpressTM bacterial mRNA enrichment kit (Ambion, Austin, TX, USA) was used to remove bacterial rRNA from the total RNA samples.
Nine libraries for RNA-seq were prepared using the Illumina TruSeqTM RNA sample prep kit with the standard low-throughput protocol. Sequencing was performed on an Illumina HiSeq2000 instrument.

tag: strain

value: Escherichia coli str. K-12 substr. MG1655

tag: genotype

value: wild type

tag: conditions

value: 100uM tropolone


title: NASH_Liver_1w_rep2

description: Gene expression at 1 week after a high-fat diet intake

source_name: NASH Liver, 1 week, replicate 2

value: liver

tag: diet

value: high-fat


title: HOVON95: Newly diagnosed MM_131

city: Rotterdam

institute: Erasmus MC

source_name: bone marrow aspirate


title: ActD_12 Hr _iN_SNCA_2COPY_PFF added_Replicate3

tag: snca genotype

tag: pff treatment

value: PFFyes

tag: timepoint


title: Toropolone rep3


title: ActD_12 Hr _iN_SNCA_2COPY_PFF added_Replicate2


title: Toropolone rep1


title: HOVON95: Newly diagnosed MM_128

tag: tissue


title: NASH_Liver_1w_rep1

source_name: NASH Liver, 1 week, replicate 1


title: HOVON95: Newly diagnosed MM_129


title: Patient 65

value: leukocytes

value: CLL


title: HOVON95: Newly diagnosed MM_125


title: Control_Liver_1w_rep1

description: Gene expression at 1 week after a control diet intake

source_name: Control Liver, 1 week, replicate 1

value: male

value: control


title: HOVON95: Newly diagnosed MM_126

value: multiple myeloma


title: Patient 64


title: ActD_12 Hr _iN_SNCA_2COPY _PFF added_Replicate1

value: Parkinson's Disease model


title: Control_Liver_1w_rep2

source_name: Control Liver, 1 week, replicate 2


title: ActD_12 Hr _iN_SNCA_2COPY _No PFF_Replicate3

value: PFFno


title: Toxoflavin rep 3

source_name: Bacterial culture with 10 uM toxoflavin

value: 10uM toxoflavin


title: Toxoflavin rep 2


title: Patient 66


title: Patient 63


title: Toxoflavin rep 1


title: Methanol rep3

source_name: Bacterial culture with methanol

value: 2% (v/v) methanol


title: Patient 62


title: ActD_12 Hr _iN_SNCA_2COPY _No PFF_Replicate1

value: Patient derived Ngn2 induced cortical neurons


title: HOVON95: Newly diagnosed MM_123

value: Male

value: bone marrow aspirate


title: Patient 61

value: Pre-diagnostic


title: Control_Liver_2w_rep1

source_name: Control Liver, 2 weeks, replicate 1


title: Methanol rep2

value: Escherichia coli str. K-12 substr. MG1655

value: wild type


title: Patient 59

source_name: Buffy coat


title: ActD_6 Hr _iN_SNCA_4COPY_PFF added_Replicate2

source_name: Patient derived Ngn2 induced cortical neurons


title: Patient 60


title: Methanol rep1


title: ActD_12 Hr _iN_SNCA_2COPY _No PFF_Replicate2


title: Patient 58


title: HOVON95: Newly diagnosed MM_121


title: HOVON95: Newly diagnosed MM_120


title: wo_sort

city: Kyoto

first: Satoshi

last: Gojo

address: 465 Kajii-cho, Kamigyo-ku

institute: Kyoto Prefectural University of Medicine

data_processing:
RNA-seq base calls were converted into FASTQ file format by bcl2fastq2 conversion software v2.20 (Illumina).
RNA-seq reads from the FASTQ files were then aligned to the reference human genome GRCh37/hg19 using TopHat2 v2.1.0 after performing quality control (QC) with FASTX Toolkit v0.0.13, FastQC v0.11.2, and PRINSEQ lite v0.20.4.
Gene expression analysis was performed based on the fragments per kilobase million (FPKM) values calculated using the RNA-seq data by Cufflinks v2.2.1.

source_name: A549 EGFP-DDX6

growth_protocol: A549 cells were grown in DMEM with 10% FBS and 1% antibiotics.

extract_protocol:
Total RNA was extracted from each samples using the TRIzol Reagent (Life technologies, Inc.) and Direct-zol™ RNA MiniPrep Kit (Zymo Research).
Libraries for next-generation sequencing were constructed using a SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio Inc.) according to the manufacturer’s instructions.

treatment_protocol: Cells (1e5/well in 6 well plate) were seeded. Next day, cells were stimulated  by Tb2 (5 ng/ml) for 2 days to induce EMT.

tag: cell line

value: PB RNA


title: ActD_6 Hr _iN_SNCA_4COPY_PFF added_Replicate1

value: PFFyes


title: wo_presort

value: Cytoplasmic RNA


title: HOVON95: Newly diagnosed MM_122

value: Female


title: ActD_6 Hr _iN_SNCA_4COPY_No PFF_Replicate2


title: HOVON95: Newly diagnosed MM_119


title: HOVON95: Newly diagnosed MM_118


title: Patient 57

value: leukocytes

value: CLL


title: ActD_6 Hr _iN_SNCA_4COPY_PFF added_Replicate3


title: HOVON95: Newly diagnosed MM_116

value: multiple myeloma


title: HOVON95: Newly diagnosed MM_117


title: ActD_6 Hr _iN_SNCA_4COPY_No PFF_Replicate3

value: Parkinson's Disease model


title: with_sort


title: Patient 56


title: ActD_6 Hr _iN_SNCA_4COPY_No PFF_Replicate1

value: PFFno


title: Patient 55


title: ActD_6 Hr _iN_SNCA_2COPY_PFF added_Replicate2


title: ActD_6 Hr _iN_SNCA_2COPY _PFF added_Replicate1


title: CNE2 HT43C 3

city: zhengzhou

first: le

middle: xiao

last: li

address: wulibao street

institute: the First Affiliated Hospital of Zhengzhou

data_processing:
Base recognition performed using CASAVA version 1.8
Use fastp software to filter the sequence to get clean reads that can be used for data analysis
The software used for sequence alignment is Hisat2, and the reference genome version used is GRCh38.91
In the application, first use Stringtie software to compare and count the fragments in each gene segment, then use the TMM algorithm for normalization, and finally calculate the FPKM value of each gene.
Genome_build: GRCh38.91
Supplementary_files_format_and_content: tab-delimited text file includes normalized FPKM values and raw fragment counts for each Sample

source_name: Nasopharyngeal carcinoma

extract_protocol:
Total RNA was extracted with AMBION AM1560 kit.
Following "TruSeq RNA Sample Preparation Guide".

value: Nasopharyngeal epithelium-derived cells

value: heat


title: CNE2 HT43C 2


title: HOVON95: Newly diagnosed MM_124


title: HOVON95: Newly diagnosed MM_114


title: HOVON95: Newly diagnosed MM_115


title: HOVON95: Newly diagnosed MM_113


title: with_presort


title: Patient 51


title: HOVON95: Newly diagnosed MM_111


title: HOVON95: Newly diagnosed MM_112


title: CNE2 HT43C 1


title: Patient 52


title: CNE2 Ctrl 3

value: control


title: Patient 50


title: CNE2 Ctrl 2


title: CNE2 Ctrl 1


title: ActD_6 Hr _iN_SNCA_2COPY _No PFF_Replicate2

value: Patient derived Ngn2 induced cortical neurons


title: ActD_6 Hr _iN_SNCA_2COPY _No PFF_Replicate1


title: ActD_6 Hr _iN_SNCA_2COPY _No PFF_Replicate3


title: ActD_6 Hr _iN_SNCA_2COPY_PFF added_Replicate3


title: Patient 53


title: Patient 49


title: ActD_3 Hr _iN_SNCA_4COPY_PFF added_Replicate3


title: Patient 54


title: HOVON95: Newly diagnosed MM_108

value: Male

value: bone marrow aspirate


title: HOVON95: Newly diagnosed MM_107


title: Patient 48

value: Pre-diagnostic


title: HOVON95: Newly diagnosed MM_110


title: ActD_3 Hr _iN_SNCA_4COPY_PFF added_Replicate2


title: Patient 47


title: HOVON95: Newly diagnosed MM_109


title: HOVON95: Newly diagnosed MM_106


title: 7_1_S88_R1_001

city: Amsterdam

first: Leandro

last: Moreno

address: Meibergdreef 9

institute: AmsterdamUMC

description: RNA-seq from peritoneal metastatic disease

data_processing:
RNA - seq transcript quantification was performed by mapping the high quality reads to the GRCh38 human transcriptome by using the software RSEM 50 and the STAR aligner
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw counts table

extract_protocol:
Frozen samples were immersed in RLT buffer (AllPrep DNA/RNA/miRNA Univers al Kit, Qiagen) and disrupted and homogenized using TissueLyser LT (Qiagen). Total RNA and DNA were isolated simultaneously from tissue lysates using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen), following the manufacturer’s instructions. The RNA and D NA concentration was measured using NanoDrop 2000 (Thermo Scientific) and Qubit fluorometer (Thermo Fisher Scientific
Libraries were prepared using Kapa mRNA HyperPrep, sequencing was performed using Illumina HiSeq (Single Read, 50 bp)

value: peritoneal metastatic disease


title: Patient 45


title: 8_2_S89_R1_001

source_name: RNA-seq from peritoneal metastatic disease


title: Patient 44


title: 6_1_S87_R1_001


title: Patient 43


title: 52_3_S86_R1_001


title: ActD_3 Hr _iN_SNCA_4COPY_No PFF_Replicate2


title: 9_2_S90_R1_001


title: ActD_3 Hr _iN_SNCA_2COPY_PFF added_Replicate3


title: 52_2_S85_R1_001


title: Patient 46


title: ActD_3 Hr _iN_SNCA_4COPY_PFF added_Replicate1


title: Patient 42


title: ActD_3 Hr _iN_SNCA_4COPY_No PFF_Replicate3


title: Patient 41


title: ActD_3 Hr _iN_SNCA_2COPY_PFF added_Replicate2


title: 52_1_S84_R1_001


title: 5_2_S83_R1_001


title: ActD_3 Hr _iN_SNCA_2COPY _PFF added_Replicate1


title: ActD_3 Hr _iN_SNCA_4COPY_No PFF_Replicate1


title: 51_3_S82_R1_001


title: Patient 39


title: ActD_3 Hr _iN_SNCA_2COPY _No PFF_Replicate3


title: ActD_3 Hr _iN_SNCA_2COPY _No PFF_Replicate2


title: 51_2_S81_R1_001


title: Patient 38


title: 51_1_S80_R1_001


title: Patient 37


title: 50_1_S79_R1_001


title: ActD_3 Hr _iN_SNCA_2COPY _No PFF_Replicate1


title: HOVON95: Newly diagnosed MM_105


title: HOVON95: Newly diagnosed MM_104


title: 49_2_S78_R1_001


title: 4_1_S63_R1_001


title: ActD_1 Hr _iN_SNCA_4COPY_PFF added_Replicate3


title: HOVON95: Newly diagnosed MM_101


title: Patient 40


title: Patient 36


title: HOVON95: Newly diagnosed MM_102


title: ActD_1 Hr _iN_SNCA_4COPY_PFF added_Replicate2


title: HOVON95: Newly diagnosed MM_103


title: HOVON95: Newly diagnosed MM_100


title: HOVON95: Newly diagnosed MM_99


title: HOVON95: Newly diagnosed MM_98


title: HOVON95: Newly diagnosed MM_97


title: HOVON95: Newly diagnosed MM_95


title: HOVON95: Newly diagnosed MM_96


title: HOVON95: Newly diagnosed MM_94


title: Patient 35


title: ActD_1 Hr _iN_SNCA_4COPY_PFF added_Replicate1


title: ActD_1 Hr _iN_SNCA_4COPY_No PFF_Replicate3


title: Patient 34


title: 48_3_S76_R1_001


title: 48_2_S75_R1_001


title: Patient 33


title: Patient 32


title: ActD_1 Hr _iN_SNCA_4COPY_No PFF_Replicate1


title: 49_1_S77_R1_001

description: RNA-seq from primary tumor

source_name: RNA-seq from primary tumor

value: primary tumor


title: Patient 31


title: 48_1_S74_R1_001


title: 47_4_S73_R1_001


title: Patient 30


title: ActD_1 Hr _iN_SNCA_2COPY_PFF added_Replicate3

value: PFFyes


title: Patient 28


title: Patient 29


title: ActD_1 Hr _iN_SNCA_2COPY_PFF added_Replicate2


title: 47_3_S72_R1_001

description: RNA-seq from primary tumor


title: ActD_1 Hr _iN_SNCA_2COPY _PFF added_Replicate1


title: ActD_1 Hr _iN_SNCA_4COPY_No PFF_Replicate2


title: 45_1b_S70_R1_001


title: ActD_1 Hr _iN_SNCA_2COPY _No PFF_Replicate3


title: 46_1b_S71_R1_001


title: Patient 27


title: 44_3_S69_R1_001


title: ActD_1 Hr _iN_SNCA_2COPY _No PFF_Replicate2


title: Patient 26


title: Patient 25


title: ActD_1 Hr _iN_SNCA_2COPY _No PFF_Replicate1


title: ActD_0 Hr _iN_SNCA_4COPY_PFF added_Replicate3


title: 44_1_S67_R1_001


title: 44_2_S68_R1_001


title: Patient 23


title: Patient 24


title: 43_1_S66_R1_001


title: ActD_0 Hr _iN_SNCA_4COPY_PFF added_Replicate2


title: Patient 22 Sample 2


title: 42_1_S65_R1_001


title: ActD_0 Hr _iN_SNCA_4COPY_PFF added_Replicate1


title: ActD_0 Hr _iN_SNCA_4COPY_No PFF_Replicate3


title: Patient 22


title: ActD_0 Hr _iN_SNCA_4COPY_No PFF_Replicate2


title: Patient 21 Sample 2


title: 40_1_S62_R1_001


title: 3_1_S48_R1_001


title: ActD_0 Hr _iN_SNCA_4COPY_No PFF_Replicate1


title: ActD_0 Hr _iN_SNCA_2COPY_PFF added_Replicate3


title: 41_1_S64_R1_001


title: 39_3_S61_R1_001

description: RNA-seq from primary tumor


title: Patient 20 Sample 2


title: ActD_0 Hr _iN_SNCA_2COPY_PFF added_Replicate2


title: HOVON95: Newly diagnosed MM_93


title: 39_1_S60_R1_001


title: Patient 21


title: Patient 20


title: HOVON95: Newly diagnosed MM_85


title: 38_3_S59_R1_001


title: HOVON95: Newly diagnosed MM_89


title: ActD_0 Hr _iN_SNCA_2COPY _PFF added_Replicate1


title: HOVON95: Newly diagnosed MM_79


title: HOVON95: Newly diagnosed MM_90


title: Patient 19 Sample 2


title: HOVON95: Newly diagnosed MM_84


title: HOVON95: Newly diagnosed MM_86


title: HOVON95: Newly diagnosed MM_81


title: HOVON95: Newly diagnosed MM_91


title: HOVON95: Newly diagnosed MM_78


title: HOVON95: Newly diagnosed MM_88


title: HOVON95: Newly diagnosed MM_75


title: HOVON95: Newly diagnosed MM_80


title: HOVON95: Newly diagnosed MM_82


title: 38_2_S58_R1_001


title: HOVON95: Newly diagnosed MM_87


title: Patient 19


title: ActD_0 Hr _iN_SNCA_2COPY _No PFF_Replicate3


title: ActD_0 Hr _iN_SNCA_2COPY _No PFF_Replicate2


title: 38_1_S57_R1_001


title: HOVON95: Newly diagnosed MM_76


title: HOVON95: Newly diagnosed MM_77


title: HOVON95: Newly diagnosed MM_92


title: HOVON95: Newly diagnosed MM_83


title: HOVON95: Newly diagnosed MM_74


title: ActD_0 Hr _iN_SNCA_2COPY_No PFF_Replicate1


title: Patient 18


title: ASC-J9 KFs

city: Tainan City

first: Yi-Kai

last: Hong

state: Please select an option below

address: No.1, Daxue Rd., East Dist.

country: Taiwan

institute: National Cheng Kung University

data_processing:
The bases with low quality and sequences from adapters in raw data were removed using the program Trimmomatic.
The filtered reads were aligned to the reference genomes using Bowtie2.
A user-friendly software application, RSEM, was applied for the quantification of transcript abundance.
Differentially expressed genes (DEGs) were identified by EBSeq.
Genome_build: hg38
Supplementary_files_format_and_content: peak text files

source_name: Keloid fibroblasts

growth_protocol: Cells are supplemented with Dulbecco’s modified Eagle’s medium (Sigma-Aldrich, St. Louis, MO) containing 10% fetal bovine serum (Invitrogen, Massachusetts, USA), 2 mM L-glutamine (Invitrogen), 100 U/ml penicillin (Sigma-Aldrich), and 100 μg/ml streptomycin (Sigma-Aldrich). The fibroblasts were generally subcultured at a 1:3 ratio when the cells reached around 80% confluence.

extract_protocol:
Total mRNA was extracted by RNeasy mini kit (Qiagen, USA)
The purified RNA was used for the preparation of the sequencing library by the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA)

treatment_protocol: NFs and KFs treated with DMSO or 10 μM ASC-J9 for 24 hours


title: Patient 17 Sample 3

first: Anton

last: Langerak

address: Doctor Molewaterplein 40

data_processing:
Library strategy: B-cell receptor repertoire
Raw FASTQ files were uploaded to the ARResT/Interrogate immunoprofiler for annotation and initial exploratory analysis. The full productive IGH repertoire for each sample was downloaded in .csv format and processed in R (R Core Team, 2020) during further analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited tekst file containing: sample,QC.status,scenario,rearrangements,raw.count,w.junction.count,w.junction.percent,artefacts.count,artefacts.percent,usable.count,usable.percent,w.most.pop.cln.s..count,w.most.pop.cln.s..percent,uniq.usable.seq.count,clonotypes.count,diversity..norm.ed..count,effective.species.count,R1.Q.mean.stdev.count,R2.Q.mean.stdev.count,joined.normally.count,joined.normally.percent,joined.loosely.count,joined.loosely.percent,total.joined.count,total.joined.percent,saved.from.unjoined.count,saved.from.unjoined.percent,low.quality..ee.nt...0.01..count,low.quality..ee.nt...0.01..percent,short...50nt..count,short...50nt..percent,annotated.count,annotated.percent,w.TR.receptor.count,w.TR.receptor.percent,w.B.chain.count,w.B.chain.percent,w.VJ.Vb..Db..Jb.count,w.VJ.Vb..Db..Jb.percent,w.VJ.Vb..Db..Jb.cln

extract_protocol:
Total  gDNA was isolated from the buffycoat DNA and 250-500 ng was amplified through multiplex PCR of IGHV-IGHD-IGHJ gene rearrangements following the BIOMED-2 protocol. After amplification, PCR products were purified on Agencourt AMPURE beads (Beckman Coulter, Brea, CA, USA) and eluted using H2O. The purified product was checked for primer dimers using the Agilent Tapestation (Agilent,Santa Clara, CA, USA).
The intitial multiplex PCR already attached the indexes to the PCR products, so library construction was simply pooling the purified PCR product in equilmolar fashion.


title: DMSO KFs

value: DMSO


title: 35_1_S54_R1_001


title: Patient 18 Sample 2


title: 36_1_S55_R1_001


title: ASC-J9 NFs

source_name: Normal fibroblasts


title: Patient 17


title: 34_1b_S53_R1_001


title: Patient 17 Sample 2


title: 37_1_S56_R1_001


title: 33_3c_S52_R1_001

description: RNA-seq from primary tumor


title: DMSO NFs


title: 33_1b_S51_R1_001


title: HOVON95: Newly diagnosed MM_72

value: Female


title: PPC1 cells, UT, LCL, 6

city: Charleston

first: Christina

last: Voelkel-Johnson

state: SC

address: 173 Ashley Ave

department: Micro/Immuno

institute: Medical University of South Carolina

data_processing:
base calling: CASAVA software
alignment: STAR software
quantification: HTSeq
differential analysis on readcounts: DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with readcounts for every gene and every sample provided as a tab delimited text file

source_name: UT, LCL

growth_protocol: 8 X 10^5 cells plated in 100 mm plate on day 1 in RPMI growth media.

extract_protocol:
Qiagen RNeasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: prostate cancer cell

tag: cell population

value: parental/mitotic

value: LCL-521 exposure 5 hours prior to harvest


title: 32_1b_S50_R1_001


title: PPC1 cells, UT, LCL, 5


title: HOVON95: Newly diagnosed MM_73

tag: gender

value: multiple myeloma


title: HOVON95: Newly diagnosed MM_71


title: Patient 16

tag: cell type

value: leukocytes

value: CLL


title: Patient 15 Diagnostic Sample

value: Diagnosis


title: HOVON95: Newly diagnosed MM_70

tag: age


title: 30_3_S47_R1_001


title: HOVON95: Newly diagnosed MM_68

tag: disease state


title: HOVON95: Newly diagnosed MM_69


title: PPC1 cells, UT, LCL, 4


title: HOVON95: Newly diagnosed MM_67


title: HOVON95: Newly diagnosed MM_66


title: 31_1_S49_R1_001


title: HOVON95: Newly diagnosed MM_65


title: PPC1 cells, UT, LCL, 1


title: Patient 15 Sample 2

tag: diagnosis


title: Patient 16 Diagnostic Sample

tag: sample type


title: Patient 16 Sample 2


title: PPC1 cells, UT, LCL, 3

tag: treatment


title: 30_2b_S46_R1_001


title: 30_1b_S45_R1_001


title: HOVON95: Newly diagnosed MM_64


title: Patient 15


title: PPC1 cells, UT, LCL, 2


title: Patient 14 Diagnostic Sample


title: 2_3_S26_R1_001


title: PPC1 cells, UT, 6

source_name: UT


title: Patient 14


title: Patient 13 Diagnostic Sample


title: 2_2_S22_R1_001


title: PPC1 cells, UT, 3


title: 2_1_S20_R1_001


title: Patient 13


title: PPC1 cells, UT, 4


title: Patient 12 Diagnostic Sample


title: PPC1 cells, UT, 2


title: HOVON95: Newly diagnosed MM_61

source_name: bone marrow aspirate


title: 28_5b_S43_R1_001


title: HOVON95: Newly diagnosed MM_60


title: Patient 12


title: PPC1 cells, UT, 1


title: HOVON95: Newly diagnosed MM_63


title: HOVON95: Newly diagnosed MM_59


title: HOVON95: Newly diagnosed MM_62


title: 28_3b_S42_R1_001


title: PPC1 cells, PGCC, LCL, 6

source_name: PGCC, LCL

value: radiation induced PGCC

value: 8 Gy radiation + LCL-521 exposure 5 hours prior to harvest


title: 28_2b_S41_R1_001

description: RNA-seq from primary tumor


title: PPC1 cells, UT, 5


title: 29_2b_S44_R1_001


title: PPC1 cells, PGCC, LCL, 5


title: 28_1b_S40_R1_001


title: HOVON95: Newly diagnosed MM_57

value: Male


title: HOVON95: Newly diagnosed MM_58

value: bone marrow aspirate


title: PPC1 cells, PGCC, LCL, 4


title: HOVON95: Newly diagnosed MM_55


title: 27_2b_S39_R1_001

description: RNA-seq from primary tumor


title: Patient 10 Sample 3

value: Pre-diagnostic


title: Patient 10 Sample 2


title: PPC1 cells, PGCC, LCL, 3


title: PPC1 cells, PGCC, LCL, 2


title: Patient 11


title: Patient 10


title: HOVON95: Newly diagnosed MM_56


title: 26_3b_S37_R1_001

value: peritoneal metastatic disease


title: Patient 11 Diagnostic Sample


title: PPC1 cells, PGCC, LCL, 1


title: Patient 9 Diagnostic Sample


title: Patient 10 Diagnostic Sample


title: 26_2_S36_R1_001


title: HOVON95: Newly diagnosed MM_54


title: 26_1_S35_R1_001


title: PPC1 cells, PGCC, 6

source_name: PGCC

value: 8 Gy radiation


title: HOVON95: Newly diagnosed MM_53


title: HOVON95: Newly diagnosed MM_52


title: HOVON95: Newly diagnosed MM_51


title: HOVON95: Newly diagnosed MM_50


title: 25_4b_S34_R1_001


title: PPC1 cells, PGCC, 5


title: Patient 9 Sample 2


title: HOVON95: Newly diagnosed MM_49


title: 25_3_S33_R1_001

description: RNA-seq from primary tumor

value: primary tumor


title: PPC1 cells, PGCC, 4


title: HOVON95: Newly diagnosed MM_48


title: 25_2_S32_R1_001


title: 27_1b_S38_R1_001


title: Patient 8


title: Patient 7 Sample 2


title: PPC1 cells, PGCC, 2


title: PPC1 cells, PGCC, 1


title: Patient 7 Diagnostic Sample


title: PPC1 cells, PGCC, 3


title: Patient 9


title: 24_1_S30_R1_001


title: U2AF2 eCLIP-seq, rep2

first: Giulia

last: Biancon

state: Connecticut

department: Internal Medicine - Yale Cancer Center

description: U2AF2 eCLIP-seq from HEL cells, biological replicate 2

data_processing:
U2AF2 eCLIP-seq reads were processed according to the pipeline reported in Biancon et al., 2022. After duplicate removal with FastUniq and adapter trimming with Cutadapt, reads were aligned to the human genome (GRCh38.p10) with STAR (v2.7.0f, --quantMode GeneCounts), using the GENCODE Release 27 for transcript annotation. Binding sites were identfied extracting the genomic position of the crosslinked nucleotide right after the end of each sequenced read. Bound junctions were confidently identified considering a nucleotide region from -40 to +10 around the 3’SS in all the annotated splice junctions in the human genome and using a coverage threshold of at least 10 reads.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: Tab-delimited text file including gene ID (column 1) and sample-specific counts of aligned eCLIP-seq reads.

source_name: Human Erythroleukemia Cell Line (HEL)

growth_protocol: RPMI 1640 10% FBS 1% L-glutamine 1% penicillin-streptomycin

extract_protocol:
Zymo RNA Clean & Concentrator-5
Cell pellets were subjected to UV-crosslinking (400 mJ/cm2 UV Stratalinker 2400, STRATAGENE), lysis and sonication. RNA was partially digested with RNase I (ThermoFisher SCIENTIFIC, Cat #AM2295). RNA-protein complexes were immunoprecipitated with 8 μg anti-U2AF2 antibody (Sigma-Aldrich, Cat #U4758) and Dynabeads Protein G (ThermoFisher SCIENTIFIC, Cat #10004D), followed by RNA linker ligation and P32-labeling. U2AF-RNA complexes were isolated by SDS-PAGE and transferred to nitrocellulose membranes. Excised membranes were treated with proteinase K and the RNA was isolated. Reverse transcription and library preparation were carried out according to the published protocol (Van Nostrand et al., 2016). Libraries were deep-sequenced on Illumina NovaSeq 6000 system, paired-end 100 bp.

tag: sequencing method

value: eCLIP-seq


title: 25_1_S31_R1_001


title: HOVON95: Newly diagnosed MM_46


title: Patient 6 Diagnostic Sample


title: 23_3_S29_R1_001


title: HOVON95: Newly diagnosed MM_47


title: Patient 7


title: U2AF2 eCLIP-seq, rep1

description: U2AF2 eCLIP-seq from HEL cells, biological replicate 1


title: M2lower

city: Bangkok

first: Sermporn

last: Thaweesapphithak

address: 34 Thanon Henri Dunant Wang Mai, Khet Pathum Wan

country: Thailand

institute: Chulalongkorn University

data_processing:
RNA-Seq Alignment program (Illumina Inc.) was used to analyze raw data and RNA-Seq Differential Expression program (Illumina Inc.) for data analysis after alignment according to the reference genome of Homo sapiens (UCSC hg19)
The upper teeth were used as a control group and the lower teeth as a comparison group. Mean count was the normalized mean count of the control and comparison groups. Genes with low mean count of below 10 were excluded.
Genes were considered true significance when p-value ≤ 0.05 and false discovery rate (FDR) ≤ 0.05.
The genes with true significance and log2 fold change (log2FC) ≤−2 or ≥2 (exhibiting 4-fold change or more) from each pair of premolar teeth and molar teeth were selected and compared.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Matrix table with normalized abundance measurements for every gene and every sample

source_name: Dental pulp cells

growth_protocol: Dental pulp cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Gibco BRL) supplemented with 10% fetal bovine serum (FBS) (Gibco), 1% L-glutamine, 100 U/ml penicillin, and 100 μg/ml streptomycin (Gibco). The cells were incubated in a 5% CO2 humidified atmosphere at 37 °C. The dental pulp cells from passage 4 were used in the study.

extract_protocol:
RNA was isolated using RNeasy Plus Mini kit (Qiagen) according to the manufacturer's protocol with DNaseI treatment. RNA was eluted from the column using nuclease free water.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MSCs

tag: cell passage

value: passage 4


title: M2upper


title: Patient 6 Sample 5


title: Patient 8 Diagnostic Sample


title: HOVON95: Newly diagnosed MM_45


title: Patient 6 Sample 4


title: HOVON95: Newly diagnosed MM_40


title: HOVON95: Newly diagnosed MM_44

value: Female


title: Patient 6 Sample 3


title: 22_4_S25_R1_001


title: 22_3b_S24_R1_001


title: M1lower


title: 23_2b_S28_R1_001


title: 23_1_S27_R1_001


title: HOVON95: Newly diagnosed MM_41


title: Patient 6 Sample 2


title: HOVON95: Newly diagnosed MM_42


title: HOVON95: Newly diagnosed MM_39


title: M1upper


title: P2lower


title: HOVON95: Newly diagnosed MM_38


title: Patient 6


title: P2upper


title: P1lower


title: 20_2_S18_R1_001


title: 20_3_S19_R1_001


title: HOVON95: Newly diagnosed MM_36


title: P1upper


title: HOVON95: Newly diagnosed MM_37


title: Patient 5 Diagnostic Sample


title: 22_2_S23_R1_001


title: 21_1_S21_R1_001


title: Patient 4 Diagnostic Sample


title: Patient 4


title: HOVON95: Newly diagnosed MM_34


title: sh-Ptbp1-7d-1

city: wenzhou

first: kankai

last: wang

address: wenzhou medical university

institute: wenzhou medical university

data_processing:
Illumina Casava1.7 software used for basecalling.
Hisat2 software is used for the sequence alignment between Clean Reads and the reference genome to obtain the position information on the reference genome or gene, as well as the unique sequence characteristics of the sequenced sample.
The FPKM value of each sample is calculated as an index to measure the transcript or gene expression level.
Genome_build: GRCh38
Supplementary_files_format_and_content: list include FPKM values for all samples

source_name: U-251 MG cell line human

extract_protocol:
TRIzol was used to extract total RNA from U251 glioma cells after infection.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human-derived U251 cell line

value: infected with sh-Ptbp1 lentivirus for 7 days


title: sh-Ptbp1-7d-2


title: HOVON95: Newly diagnosed MM_35

value: multiple myeloma


title: 1_2b_S8_R1_001


title: sh-Ptbp1-7d-3


title: 1_1b_S5_R1_001


title: Patient 3

value: leukocytes

value: CLL


title: 20_1_S17_R1_001


title: sh-Ptbp1-3d-2

value: infected with sh-Ptbp1 lentivirus for 3 days


title: Patient 3 Diagnostic Sample

value: Diagnosis


title: 18_1_S15_R1_001


title: sh-Ptbp1-3d-1


title: Patient 2 Sample 2


title: 17_1_S14_R1_001


title: sh-Ptbp1-3d-3


title: Patient 5 Sample 2


title: 19_1_S16_R1_001


title: 1_3b_S10_R1_001


title: Patient 5


title: sh-Luci-3d-2

value: infected with sh-Luci lentivirus for 3 days


title: 16_1_S13_R1_001


title: 15_2_S12_R1_001


title: Patient 2


title: HOVON95: Newly diagnosed MM_33

value: bone marrow aspirate


title: Patient 2 Diagnostic Sample


title: sh-Luci-3d-3


title: Patient 1 Diagnostic Sample


title: HOVON95: Newly diagnosed MM_43


title: HOVON95: Newly diagnosed MM_32


title: HOVON95: Newly diagnosed MM_30

value: Male


title: HOVON95: Newly diagnosed MM_28


title: HOVON95: Newly diagnosed MM_29


title: Patient 1

value: Pre-diagnostic


title: HOVON95: Newly diagnosed MM_24


title: SZ30_TCR

city: Pittsburgh

first: Patrizia

last: Fuschiotti

address: 200 Lothrop St

institute: University of Pittsburgh

data_processing:
Chromium scRNA-seq data produced by the 10X Chromium Platform were processed to generate sample-specific fastq files.
Processed reads were then examined by quality metrics, mapped to a reference human genome using RNA-seq aligner STAR and assigned to individual cells of origin according to the cell specific barcodes, using the Cell Ranger pipeline (10X Genomics).
To ensure that PCR amplified transcripts were counted only once, only single UMIs were counted for gene expression level 10. In this way, cell x gene UMI counting matrices were generated for downstream analyses.
Seurat, an R package developed for single-cell analysis, was used to identify distinct cell populations and visualize cell clusters in graphs. Specifically, the UMI matrix was filtered such that only cells expressing at least 200 genes were utilized in downstream analysis.
Unwanted sources of variation were regressed out of the data by constructing linear models to predict gene expression based on the number of UMIs per cell as well as the percentage of mitochondrial gene content.
Hashtags were demultiplexed based on the Seurat package, https://satijalab.org/seurat/articles/hashing_vignette.html
Genome_build: GrCh38A genome
Supplementary_files_format_and_content: H5 files for gene expression, CSV files for TCR outputs

source_name: CTCL PBMCs

extract_protocol:
Skin biopsies were minced and digested enzymatically (Whole Dissociation Skin Kit, Miltenyi Biotec) for 2 hours at 37°C and further dispersed using the Miltenyi gentleMACS Octo Dissociator. Normal skin biopsies were hashed together 2 at a time per protocol: https://www.biolegend.com/en-us/protocols/totalseq-b-or-c-with-10x-feature-barcoding-technology Normal Sample 1 and 2 are labeled with HTO1 and HTO2 respectively. Normal sample 3 and 4 are labeled with HTO9 and HTO10 respectively. PBMCs were acquired from whole blood samples using Ficoll. Experimental procedures followed established techniques using the Chromium Single Cell 5’ Library V1 kit (10x Genomics).
Experimental procedures followed established techniques using the Chromium Single Cell 5’ Library V1 kit +V(D)J Enrichment Kit, Human T Cell (10x Genomics).
Single Cell 10x Genomics 5' Library V1 Chemistry +V(D)J Enrichment Kit, Human T Cell

tag: health status

value: Sezary Syndrome


title: HOVON95: Newly diagnosed MM_31


title: 14_1b_S11_R1_001

value: peritoneal metastatic disease


title: HOVON95: Newly diagnosed MM_27


title: HOVON95: Newly diagnosed MM_26


title: sh-Luci-3d-1


title: Control 123

source_name: Buffy coat

value: healthy

value: Control


title: 12_2_S7_R1_001

description: RNA-seq from primary tumor

value: primary tumor


title: MF19_TCR

source_name: Skin Tumor

value: Mycosis fungoides


title: 10_4_S3_R1_001


title: Control 120


title: SZ22_TCR


title: HOVON95: Newly diagnosed MM_23


title: Control 119


title: 10_3_S2_R1_001


title: SZ30_GEX


title: 10_2_S1_R1_001


title: Control 118


title: SZ29_MF25_GEX_HTO

description:
Hashtags_feature_reference.csv
SZ29 and MF25 are hashtagged together. SZ29 uses HTO1 and MF25 uses HTO2. Both samples are from the same patient

source_name: CTCL PBMCs, Skin Tumor

value: Sezary Syndrome, Mycosis fungoides


title: HB1_2_3_GEX_HTO

description:
Hashtags_feature_reference.csv
HB1, HB2, and HB3 are hashtagged together using HTO1, HTO2, and HTO3 respectively

source_name: Healthy PBMCs

value: Healthy Control


title: 12_1_S6_R1_001

source_name: RNA-seq from peritoneal metastatic disease


title: Control 121


title: Control 122