title: LDB1_ChIP_WT_rep5

description:
Library name: LDB1_ChIP_WT_rep5
LDB1_ChIP_WT_rep5_RPKM.bw
LDB1_ChIP_WT_merge_RPKM.bw
LDB1_ChIP_WT_rep5_DESeq2_normalized.bw
LDB1_ChIP_WT_merge_DESeq2_normalized.bw
LDB1_ChIP_WT_rep5_minus_estradiol_DESeq2_normalized.bw
LDB1_ChIP_WT_merge_minus_estradiol_DESeq2_normalized.bw


title: NOVA55_N-Brush_Phase_2_SD_-1

status: Public on Jul 23 2025

type: RNA

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

country: USA

institute: Institute for Systems Biology

description: Gene expression profiling of nasal epithelium from influenza infected humans

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Homo sapiens

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from nasal epithlium using Qiagen RNA isolation kit according to manufacturer's instructions.RNA quality was assessed using Agilent Bioanalyzer.

treatment_protocol: Nasal epithelium cells  collected from humans  and stored in RNALater tubes  according to manufacturer's instructions.

tag: treatment

value: challenged with influenza

tag: tissue

value: Nasal epithelium

tag: study group

value: Unvaccinated

tag: study date

value: SD -1


title: NOVA62_N-Brush_Phase_2_SD_-1


title: kidney biopsy N718

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

source_name: kidney biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: All human kidney biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

tag: mmdx (abmr, mixed, nr[no rejection], pabmr, ptcmr, tcmr)

value: ABMR


title: LDB1_ChIP_WT_rep3

type: SRA

city: Philadelphia

first: Xiaokang

last: Wang

state: PA

address: 315 A  Abramson Research Center, 3615 Civic Center Blvd.

department: Hematology

institute: Children's hospital of Philadelphia

description:
Library name: LDB1_ChIP_WT_rep3
LDB1_ChIP_WT_rep3_RPKM.bw
LDB1_ChIP_WT_merge_RPKM.bw
LDB1_ChIP_WT_rep3_DESeq2_normalized.bw
LDB1_ChIP_WT_merge_DESeq2_normalized.bw
LDB1_ChIP_WT_rep3_minus_estradiol_DESeq2_normalized.bw
LDB1_ChIP_WT_merge_minus_estradiol_DESeq2_normalized.bw

library_source: genomic

data_processing:
The ChIP-seq data was processed by using nf-core/chipseq pipeline 2.0.0.
Assembly: mm9
Supplementary files format and content: bw: tracks of ChIP-seq signals

molecule: genomic DNA

organism: Mus musculus

source_name: cell line

extract_protocol:
Dual crosslinked DNA from lysed cells was sonicated using the Bioruptor Pico, immunoprecipitated, and then extracted using the QIAquick PCR Purification kit (Qiagen 28106).
The NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7635) was used to prepare libraries using unique dual-indexed primers (NEB E6440).

treatment_protocol: The cells were either untreated, or treated with 12h estradiol, or 0h/1h/2h DMSO, or 0h/1h/2h dTAGV-1, 0h/4h Auxin.

value: cell line

tag: cell line

tag: cell type

value: Erythroblast

tag: genotype

value: WT


title: NOVA48_N-Brush_Phase_2_SD_-1


title: NOVA36_N-Brush_Phase_2_SD_-1


title: kidney biopsy N717

value: NR


title: MD+CA4

city: College Station

first: Aditya

middle: D

last: Joshi

state: Texas

address: 560 Raymond Stotzer Pkwy

institute: Texas A&M University

library_source: transcriptomic

data_processing:
quality of fastqs were checked and processed with the fastp
reads were aligned with salmon 1.10.3
DESeq2 was utilized for stats and foldchange
Assembly: GRCm39 vM35
Supplementary files format and content: sf

source_name: Liver

extract_protocol:
RNA was extrated from snap-frozen liver tissues using Trizol.
Library construction was done using 500 ng of total RNA. Libraries were constructed using NEBNext poly(A) mRNA isolation kit followed directly by IDT’s XGen Broad Range RNA Library Prep Kit and the established protocols. Each of the libraries was indexed during library construction to multiplex the sequencing.

treatment_protocol: For the MD + CA group, 12 mg/kg body weight CA (in 0.2% DMSO) was intraperitoneally injected thrice a week on Mondays, Wednesdays, and Fridays for the entire duration of the study (20-weeks). Mice in the MD group were treated with vehicle (0.2% DMSO + 98.8% saline) via i.p. three days a week (Mondays, Wednesdays, and Fridays) for 20 weeks.

value: Liver

tag: Sex

value: male

tag: age

value: Eight-week-old

value: AhR-floxed mice

value: MD+cinnabarinic acid


title: MD+CA2


title: kidney biopsy N715


title: NOVA81_N-Brush_Phase_2_SD_-1


title: NOVA78_N-Brush_Phase_2_SD_-1


title: kidney biopsy N716


title: MD+CA1


title: MD4

value: MD


title: MD3


title: MD2


title: NOVA75_N-Brush_Phase_2_SD_-1


title: kidney biopsy N713


title: MD+CA3


title: kidney biopsy N714


title: NOVA70_N-Brush_Phase_2_SD_-1


title: NOVA58_N-Brush_Phase_2_SD_-1


title: kidney biopsy N710


title: kidney biopsy N712

value: Mixed


title: NOVA82_N-Brush_Phase_2_SD_-1


title: MD1


title: CD4


title: NOVA64_N-Brush_Phase_2_SD_-1


title: CD3


title: CD2


title: NOVA57_N-Brush_Phase_2_SD_-1


title: kidney biopsy N708


title: CD1


title: kidney biopsy N709


title: NOVA59_N-Brush_Phase_2_SD_-1


title: kidney biopsy N707


title: kidney biopsy N706

value: pABMR


title: SNL230508VC_HA_baboon_5_LAMY_1_NeuN_10x_L1

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

library_source: transcriptomic single cell

data_processing:
FASTQ files were pre-processed with the 10x CellRanger pipeline
Human reads were aligned to reference genome GRCh38, rhesus macaque reads were aligned to reference genome Mmul_10, and Olive Baboon reads with aligned to refernce genome Panubis1.0.
Assembly: GRCh38, Mmul_10, and Panubis1.0
Supplementary files format and content: Raw FASTQ files and data processed with the 10x CellRanger pipeline with barcode, feature, and matrix files for each sample.

molecule: polyA RNA

organism: Papio anubis

source_name: brain (amygdala)

extract_protocol:
For human samples, the amygdala was dissected from fresh frozen postmortem human tissue and 100 micron coronal sections of amygdala from fresh frozen postmortem human tissue were obtained by cryosectioning. For nonhuman primates, coronal brain blocks were flash-frozen immediately prior to tissue punches localized to specific amygdala subregions. All nuclei were isolated and barcoded with 10x Genomics Chromium.
Libraries were prepared using 10x Chromium Next GEM Single Cell 3’ v3.1 (dual-index) kit according to manufacturer's instructions.
single-nucleus RNA-sequencing

value: brain (amygdala)


title: SNL230508VC_HA_baboon_5_LAMY_1_NeuN_plus_DAPI_10x_L1


title: kidney biopsy N711


title: SNL230508VC_HA_baboon_5_BAMY_1_NeuN_plus_DAPI_10x_L1


title: kidney biopsy N705


title: LDB1_ChIP_WT_rep2

description:
Library name: LDB1_ChIP_WT_rep2
LDB1_ChIP_WT_rep2_RPKM.bw
LDB1_ChIP_WT_merge_RPKM.bw
LDB1_ChIP_WT_rep2_DESeq2_normalized.bw
LDB1_ChIP_WT_merge_DESeq2_normalized.bw
LDB1_ChIP_WT_rep2_minus_estradiol_DESeq2_normalized.bw
LDB1_ChIP_WT_merge_minus_estradiol_DESeq2_normalized.bw


title: NOVA77_N-Brush_Phase_2_SD_-1

value: challenged with influenza

value: Nasal epithelium


title: LDB1_ChIP_WT_rep1

description:
Library name: LDB1_ChIP_WT_rep1
LDB1_ChIP_WT_rep1_RPKM.bw
LDB1_ChIP_WT_merge_RPKM.bw
LDB1_ChIP_WT_rep1_minus_estradiol_DESeq2_normalized.bw
LDB1_ChIP_WT_merge_minus_estradiol_DESeq2_normalized.bw


title: SNL230508VC_AN__baboon_2_LAMY_1_NeuN_10x_L1


title: SNL230508VC_AN__baboon_2_BAMY_2_NeuN_10x_L1


title: SNL230508VC_HA_baboon_5_BAMY_1_NeuN_10x_L1


title: SNL230508VC_AN__baboon_2_BAMY_1_NeuN_10x_L1


title: Vehicle_1

city: Richmond

first: Grayson

middle: Welch

last: Way

email: waygw@vcu.edu, waygw@outlook.com

state: Virginia

address: 1217 E Marshall Street Room 534

department: Microbiology and Immunology

institute: VCU

description: Library name: SOA_V1_S1

data_processing:
Samples were aligned to the GRCh38 Human primary assembly genome accessed at https://ftp.ensembl.org/pub/release-108/fasta/homo_sapiens/dna/ using STAR aligner version 2.7.9a, with default parameters. No trimming was required.
The featureCounts tool from the SourceForge Subread package was used to generate the raw counts. The reads were counted over exons using the ensembl gtf file for Homo sapiens, GRCh38 assembly, can be accessed at: https://ftp.ensembl.org/pub/release-108/gtf/homo_sapiens/ In addition to default parameters, these were used for featurecounts: "-T 16 -F GTF -t exon -g gene_id -p --countReadPairs"
The Deseq2 R library was used to perform differential expression with the default DESeq2 "median of ratios" method for count normalization.Gene prefiltering was performed as described in the DESeq2 documentation. Genes were excluded if they do not have three or more samples with a read count of 10 or greater. Differential expression results were considered significant if the Benjamini-Hochberg adjusted p-value (padj) is less than or equal to 0.05 and the absolute log2 fold change is greater than 0.58 (corresponding to an absolute fold change of 1.5).
Assembly: Homo sapiens (human) genome assembly GRCh38 (hg38)
Supplementary files format and content: csv file with raw counts for each sample

source_name: H69 cholangiocyte

growth_protocol: H69 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM)/F12 supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, adenine, insulin, epinephrine, T3-T, hydrocortisone, and epidermal growth factor.

extract_protocol:
RNA was extracted using Trizol Reagent following manufacturer's protocl
Libraries prepared with 2S Plus DNA library kit from IDT

treatment_protocol: Following a 6 hour serum starvation, cells were treated in serum free media

value: H69 cholangiocyte

value: biliary epithelial cell


title: Vehicle_3

description: Library name: SOA_V3_S9


title: Vehicle_2

description: Library name: SOA_V2_S5


title: kidney biopsy N704


title: TGFb_3

description: Library name: SOA_TGFb3_S11


title: NOVA73_N-Brush_Phase_2_SD_-1

value: Unvaccinated

value: SD -1


title: NOVA68_N-Brush_Phase_2_SD_-1


title: TGFb_1

description: Library name: SOA_TGFb1_S3


title: TGFb_2

description: Library name: SOA_TGFb2_S7


title: TGFb_Aram_3

description: Library name: SOA_TGFb_Aram3_S12


title: TGFb_Aram_2

description: Library name: SOA_TGFb_Aram2_S8


title: NOVA80_N-Brush_Phase_2_SD_-1


title: kidney biopsy N702


title: Aram_3

description: Library name: SOA_Aram3_S10


title: Aram_2

description: Library name: SOA_Aram2_S6


title: Aram_1

description: Library name: SOA_Aram1_S2


title: kidney biopsy N700


title: kidney biopsy N703

value: ABMR


title: NOVA71_N-Brush_Phase_2_SD_-1


title: NOVA72_N-Brush_Phase_2_SD_-1


title: kidney biopsy N699

value: NR


title: kidney biopsy N701


title: Intraheptaic Cholangiocyte Organoids Hepatocyte-like, Donor HNN

city: Nijmegen

first: Richard

last: Bartfai

state: Gelderland

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences

description: Library name: ICO_HEP_Donor3

data_processing:
Fastq files from sequencing were evaluated for quality using the FASTQC package (ver. 0.11.9)
Trim-galore package (ver. 0.6.7) was used to trim off adapter sequence and bases with quality score <30
Trimmed fastq files were aligned against the Homo sapiens genome reference (GRCh38 primary assembly fasta) using the splice-aware STAR aligner (ver. 2.7.10a)
The aligned bam files were filtered for uniqueness and high mapping quality (samtools view -q 255) using the samtools package (ver. 1.15.1)
The filtered bam files were processed for removing duplicate alignments using a script implementing sort, fixmate and markduplicate functions in samtools.
Gene-counts were generated using featureCounts (ver. 2.0.1 from subread package) in a strandedness and paired end aware manner (featureCounts -s 2 -p -B)
Differential gene expression analysis was performed in RStudio (R version 4.3.3, “Angel Food Cake”) using the Deseq2 package (ver. 1.40.2). QC poor HEMd10_Donor1 and HMMd20_Donor3 datapoints were filtered out and not analysed
Assembly: Homo sapiens GRCh38 primary assembly
Supplementary files format and content: csv file with deseq2 normalization processed counts
Supplementary files format and content: csv file with batch-corrected (limma) counts

source_name: Intrahepatic Cholangiocyte Organoids in Maturation Medium

extract_protocol:
Total RNA was isolated from organoids, tissue and primary cells using the RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions. The isolated total RNA was passed through an additional round of DNase treatment using the Zymo Research Direct-zol RNA Miniprep kit (Cat. #R2050)
250ng of total RNA was used as input per sample to prepare mRNA library with the Kapa mRNA HyperPrep Kit (Roche Cat. #08098123702). 12 PCR cycles were used to generate the amplified cDNA library as per the kit recommendations.


title: Intraheptaic Cholangiocyte Organoids Hepatocyte-like, Donor XEN

description: Library name: ICO_HEP_Donor2

value: Intrahepatic Cholangiocyte Organoids in Maturation Medium


title: TGFb_Aram_1

description: Library name: SOA_TGFb_Aram1_S4


title: Intraheptaic Cholangiocyte Organoids in Expansion Medium, Donor HNN

description: Library name: ICO_EM_Donor3

source_name: Intrahepatic Cholangiocyte Organoids in Expansion Medium


title: Intraheptaic Cholangiocyte Organoids in Expansion Medium, Donor XEN

description: Library name: ICO_EM_Donor2

value: Intrahepatic Cholangiocyte Organoids in Expansion Medium


title: kidney biopsy N698

value: TCMR


title: day 20 Hepato-biliary Organoids in Maturation Medium, Donor HNN

description: Library name: HMMd20_Donor3

source_name: Hepato-Biliary Organoids in Maturation Medium


title: day 20 Hepato-biliary Organoids in Maturation Medium, Donor XEN

description: Library name: HMMd20_Donor2

value: Hepato-Biliary Organoids in Maturation Medium


title: Intraheptaic Cholangiocyte Organoids Hepatocyte-like, Donor 16087

description: Library name: ICO_HEP_Donor1


title: kidney biopsy N696


title: kidney biopsy N697


title: day 20 Hepato-biliary Organoids in Maturation Medium, Donor 16087

description: Library name: HMMd20_Donor1


title: kidney biopsy N695


title: LPS_HI biol rep 6

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: Library name: HSA_23

data_processing:
QC with fastQC (v0.11.9) and multiQC (v1.14). Alignment with kallisto (v0.48.0), executed with SnakeMake (v7.20.0).
Assembly: mRatBN7.2
Supplementary files format and content: DESeq2_removedbatch_log_2025-04-15.csv

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
RNA was isolated using Trizol (Thermo Scientific). 500 ng of total RNA was used for library construction.
Libraries were constructed using the TruSeq RNA Sample Preparation v2 Kit (Illumina) using the low-throughput protocol.

value: Brain

value: Microglia


title: LPS_HI biol rep 5

description: Library name: HSA_22


title: day 10 Hepato-biliary Organoids in Maturation Medium, Donor XEN

description: Library name: HMMd10_Donor2


title: kidney biopsy N694


title: Intraheptaic Cholangiocyte Organoids in Expansion Medium, Donor 16087

description: Library name: ICO_EM_Donor1


title: LPS_HI biol rep 4

description: Library name: HSA_21


title: day 10 Hepato-biliary Organoids in Maturation Medium, Donor HNN

description: Library name: HMMd10_Donor3


title: kidney biopsy N690


title: kidney biopsy N691


title: kidney biopsy N693


title: day 20 Hepato-biliary Organoids in Expansion Medium, Donor HNN

description: Library name: HEMd20_Donor3

source_name: Hepato-Biliary Organoids in Expansion Medium


title: day 20 Hepato-biliary Organoids in Expansion Medium, Donor XEN

description: Library name: HEMd20_Donor2

value: Hepato-Biliary Organoids in Expansion Medium


title: NaCl_HI biol rep 6

description: Library name: HSA_20


title: day 20 Hepato-biliary Organoids in Expansion Medium, Donor 16087

description: Library name: HEMd20_Donor1


title: day 10 Hepato-biliary Organoids in Expansion Medium, Donor HNN

description: Library name: HEMd10_Donor3


title: NaCl_HI biol rep 5

description: Library name: HSA_19


title: day 10 Hepato-biliary Organoids in Expansion Medium, Donor XEN

description: Library name: HEMd10_Donor2


title: Case #4, ARMS FFPE tissue, Female, 0.92 years old

type: genomic

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to either Illumina HumanMethylation450 BeadChip or Illumina Infinium MethylationEPIC v1 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan

data_processing: RStudio (R package ChAMP v2.32.0)

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from FFPE samples using Resnova MagPurix FFPE DNA Extraction Kit according to standard instructions.

tag: sample type

value: FFPE

value: Female

value: 0.92 years old


title: kidney biopsy N689


title: NaCl_HI biol rep 4

description: Library name: HSA_18


title: Hepatic Spheroids, Donor HNN

description: Library name: HSM_Donor3

source_name: Spheroids derived from Primary Human Hepatocytes


title: NOVA37_N-Brush_Phase_2_SD_-1

value: challenged with influenza

value: Nasal epithelium


title: day 10 Hepato-biliary Organoids in Expansion Medium, Donor 16087

description: Library name: HEMd10_Donor1


title: kidney biopsy N687


title: LPS biol rep 5

description: Library name: HSA_17


title: Hepatic Spheroids, Donor 16087

description: Library name: HSM_Donor1

value: Spheroids derived from Primary Human Hepatocytes


title: kidney biopsy N692

value: pABMR


title: kidney biopsy N688


title: Case #3, ARMS FFPE tissue, Female, 0.5 years old

source_name: ARMS FFPE tissue, Female, 0.5 years old

value: 0.5 years old


title: Case #9, ARMS FFPE tissue, Male, 17 years old

source_name: ARMS FFPE tissue, Male, 17 years old

value: Male

value: 17 years old


title: Case #8, ARMS FFPE tissue, Male, 15 years old

source_name: ARMS FFPE tissue, Male, 15 years old

value: 15 years old


title: Primary Human Hepatocytes, Donor HNN

description: Library name: PHH_Donor3

source_name: Primary human hepatocytes

value: Primary human hepatocytes


title: Hepatic Spheroids, Donor XEN

description: Library name: HSM_Donor2


title: Sham biol rep 6

description: Library name: HSA_15


title: kidney biopsy N685

value: NR


title: Psoriasis Lesioned DOI 3

city: Taipei City

first: Yeh Fong

last: Tan

state: Taipei

address: No. 128, Section 2, Academia Rd, Nangang District

department: Institute of BioMedical Sciences

country: Taiwan

institute: Academia Sinica

data_processing:
Combination of Ubuntu 22.04.1 LTS, Trimmomatic, Hisat2, SAMtools, StringTie and prepDE python package.
Separate fastq files are merged using Terminal of Ubuntu.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (MinLen: 36, Phred33).
Trimmed sequence reads were mapped to Homo_sapiens.GRCh38.109.gtf using Hisat2.
Aligned sequence were converted from SAM to BAM using SAMtools. Read count extraction was performed using StringTie. Files are then converted into CSV format using prepDE.py3 package.
Assembly: Homo_sapiens.GRCh38.109.gtf.gz
Supplementary files format and content: tab delimited text file. Sum of raw counts for each sample.

source_name: Skin

extract_protocol:
RNA from isolated Langerhans cells was extracted using R2060 DirectZol RNA MicroPrep kit (Zymo Research). 10 to 70 ng of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTer Stranded RNA-Seq Kit according to manufacturer's protocols.

treatment_protocol: We treated excised human skin (either healthy or lesioned psoriatic skin) with PBS or DOI (10mg/mL) for 24 hours before extracting RNA.

value: Skin

value: DOI-treated


title: kidney biopsy N686


title: Case #6, ARMS FFPE tissue, Male, 15 years old


title: Case #7, ARMS FFPE tissue, Male, 14 years old

source_name: ARMS FFPE tissue, Male, 14 years old

value: 14 years old


title: Psoriasis Lesioned PBS 3

value: PBS-treated


title: Case #5, ARMS FFPE tissue, Female, 16 years old

source_name: ARMS FFPE tissue, Female, 16 years old

value: FFPE

value: 16 years old


title: Primary Human Hepatocytes, Donor XEN

description: Library name: PHH_Donor2


title: LPS biol rep 4

description: Library name: HSA_16

value: Brain

value: Microglia


title: Sham biol rep 5

description: Library name: HSA_14


title: Psoriasis Lesioned DOI 2


title: Psoriasis Lesioned DOI 1


title: Psoriasis Lesioned PBS 1


title: Sham biol rep 4

description: Library name: HSA_13


title: Psoriasis Lesioned PBS 2


title: LPS_HI biol rep 3

description: Library name: HSA_12


title: Case #1, ARMS FFPE tissue, Male, 0.67 years old

source_name: ARMS FFPE tissue, Male, 0.67 years old

value: 0.67 years old


title: Case #10, ARMS FFPE tissue, Female, 10 years old

source_name: ARMS FFPE tissue, Female, 10 years old

value: Female

value: 10 years old


title: Healthy DOI 3


title: Healthy PBS 3


title: Case #2, ARMS FFPE tissue, Male, 0.83 years old

source_name: ARMS FFPE tissue, Male, 0.83 years old

value: 0.83 years old


title: kidney biopsy N683

source_name: kidney biopsy

value: Mixed


title: LPS_HI biol rep 2

description: Library name: HSA_11


title: kidney biopsy N684


title: kidney biopsy N681

value: TCMR


title: kidney biopsy N682


title: LPS_HI biol rep 1

description: Library name: HSA_10


title: Healthy DOI 2


title: Healthy PBS 2


title: Healthy DOI 1


title: NaCl_HI biol rep 3

description: Library name: HSA_09


title: Primary Human Hepatocytes, Donor 16087

description: Library name: PHH_Donor1


title: Healthy PBS 1


title: NaCl_HI biol rep 2

description: Library name: HSA_08


title: PTL_patient_548_1

city: Durham

first: Zijun

middle: Yidan

last: Xu-Monette

state: North Carolina

address: 905 S. Lasalle Street

department: Department of Pathology

institute: Duke University

description:
Library name: 561-HTG_548_1
PTL_OS_clinical_data.xlsx

data_processing:
Raw data count
CPM standarization
Normalization using edgeR R packages from Bioconductor.
The variance stabilizing log2 was transformed using the DESeq2 Bioconductor package workflow
Differentially expressed microRNAs between two groups were identified with absolute log2 fold change >1.0 and false discovery rate (FDR) <0.05 (Benjamini-Hochberg corrected p-value), and displayed in heatmaps as row-scaled normalized counts. Unsupervised clustering was performed and visualized using CLUSTER 3.0 software and JAVA TREEVIEW.
Assembly: GRCh37
Supplementary files format and content: excel spread sheet listing raw count of each gene/miRNA for each patient
Supplementary files format and content: excel spread sheet listing normalized count data for each patient only for cases passed quality control.

source_name: testicular lymphoma FFPE tissue

extract_protocol:
Total RNA was isolated from FFPE samples and QIAGEN’s miRNeasy FFPE kit according to the manufacturer’s protocol
Lysates from FFPE tissue samples were run on the HTG EdgeSeq Processor (HTG Molecular Diagnostics, Tucson, AZ) using the miRNA whole transcriptome assay in which an excess of nuclease protection probes (NPPs) complimentary to each miRNA hybridize to their target. S1 nuclease then removes un-hybridized probes and RNA leaving behind only NPPs hybridized to their targets in a 1-to-1 ratio. Samples were individually barcoded (using a 16-cycle PCR reaction to add adapters and molecular barcodes), individually purified using AMPure XP beads (Beckman Coulter, Brea, CA) and quantitated using a KAPA Library Quantification kit (KAPA Biosystems, Wilmington, MA).
an excess of nuclease protection probes (NPPs) complimentary to each miRNA hybridize to their target. S1 nuclease then removes un-hybridized probes and RNA leaving behind only NPPs hybridized to their targets in a 1-to-1 ratio

value: testicular lymphoma FFPE tissue


title: PTL_patient_571_1

description:
Library name: 561-HTG_571_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_552_1

description:
Library name: 561-HTG_552_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_544_1

description:
Library name: 561-HTG_544_1
PTL_OS_clinical_data.xlsx


title: NaCl_HI biol rep 1

description: Library name: HSA_07


title: PTL_patient_549_1

description:
Library name: 561-HTG_549_1
PTL_OS_clinical_data.xlsx


title: LPS biol rep 3

description: Library name: HSA_06


title: PTL_patient_561_1

description:
Library name: 561-HTG_561_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_545_1

description:
Library name: 561-HTG_545_1
PTL_OS_clinical_data.xlsx


title: LPS biol rep 2

description: Library name: HSA_05


title: LPS biol rep 1

description: Library name: HSA_04


title: PTL_patient_555_1

description:
Library name: 561-HTG_555_1
PTL_OS_clinical_data.xlsx


title: kidney biopsy N678


title: PTL_patient_556_1

description:
Library name: 561-HTG_556_1
PTL_OS_clinical_data.xlsx


title: kidney biopsy N680


title: kidney biopsy N679

value: ABMR


title: day 10 Hepato-biliary Organoids in Maturation Medium, Donor 16087

description: Library name: HMMd10_Donor1

value: Hepato-Biliary Organoids in Maturation Medium


title: Sham biol rep 3

description: Library name: HSA_03


title: PTL_patient_557_1

description:
Library name: 561-HTG_557_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_559_1

description:
Library name: 561-HTG_559_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_554_1

description:
Library name: 561-HTG_554_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_562_1

description:
Library name: 561-HTG_562_1
PTL_OS_clinical_data.xlsx


title: kidney biopsy N677

value: NR


title: PTL_patient_567_1

description:
Library name: 561-HTG_567_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_564_1

description:
Library name: 561-HTG_564_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_572_1

description:
Library name: 561-HTG_572_1
PTL_OS_clinical_data.xlsx


title: Sham biol rep 2

description: Library name: HSA_02


title: kidney biopsy N675


title: Sham biol rep 1

description: Library name: HSA_01


title: PTL_patient_542_1

description:
Library name: 561-HTG_542_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_547_1

description:
Library name: 561-HTG_547_1
PTL_OS_clinical_data.xlsx


title: kidney biopsy N676


title: Sham_OLE-23-58

city: Seoul

first: UnHo

last: Kang

address: 15F, 241, Gangnam-daero, Seocho-gu

country: South Korea

institute: Arontier

data_processing:
sequence file was checked for quality with FastQC
alignment was processed by STAR 2 pass
Assembly: rn6
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: distal intestine

extract_protocol:
Total RNA was harvested using Rneasy mini kit (Qiagen).
Total RNA sequencing libraries were generated using Illumina TruSeq Stranded Total RNA Sample prep kit with Ribo-zero Human/Mouse/Rat.

value: distal intestine

value: sham surgery


title: PTL_patient_558_1

description:
Library name: 561-HTG_558_1
PTL_OS_clinical_data.xlsx


title: kidney biopsy N674


title: PTL_patient_569_1

description:
Library name: 561-HTG_569_1
PTL_OS_clinical_data.xlsx


title: kidney biopsy N670


title: Sham_OLE-22-48


title: PTL_patient_568_1

description:
Library name: 561-HTG_568_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_563_1

description:
Library name: 561-HTG_563_1
PTL_OS_clinical_data.xlsx


title: kidney biopsy N671


title: PTL_patient_59_1

description:
Library name: 559-PTL_59_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_93_1

description:
Library name: 559-PTL_93_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_56_1

description:
Library name: 559-PTL_56_1
PTL_OS_clinical_data.xlsx


title: Nonglucotonic_OLE-13-34

source_name: non-glucotonic sections of the intestine

value: RYGB surgery


title: Sham_OLE-4-3


title: PTL_patient_75_1

description:
Library name: 559-PTL_75_1
PTL_OS_clinical_data.xlsx


title: kidney biopsy N672

value: pABMR


title: kidney biopsy N673


title: Nonglucotonic_OLE-19-38-39

value: non-glucotonic sections of the intestine


title: PTL_patient_78_1

description:
Library name: 559-PTL_78_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_65_1

description:
Library name: 559-PTL_65_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_96_1

description:
Library name: 559-PTL_96_1
PTL_OS_clinical_data.xlsx


title: Nonglucotonic_OLE-16-54


title: Nonglucotonic_OLE-18-39


title: PTL_patient_76_1

description:
Library name: 559-PTL_76_1
PTL_OS_clinical_data.xlsx


title: Nonglucotonic_OLE-13-33


title: PTL_patient_71_1

description:
Library name: 559-PTL_71_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_63_1

description:
Library name: 559-PTL_63_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_80_1

description:
Library name: 559-PTL_80_1
PTL_OS_clinical_data.xlsx


title: kidney biopsy N668


title: PTL_patient_87_1

description:
Library name: 559-PTL_87_1
PTL_OS_clinical_data.xlsx


title: Glucotonic_OLE-13-38-L007

source_name: glucotonic sections of the intestine

value: glucotonic sections of the intestine


title: Glucotonic_OLE-19-L006


title: PTL_patient_68_1

description:
Library name: 559-PTL_68_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_84_1

description:
Library name: 559-PTL_84_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_67_1

description:
Library name: 559-PTL_67_1
PTL_OS_clinical_data.xlsx


title: Glucotonic_OLE-18-L004


title: PTL_patient_57_1

description:
Library name: 559-PTL_57_1
PTL_OS_clinical_data.xlsx


title: Glucotonic_OLE-16-L004


title: PTL_patient_64_1

description:
Library name: 559-PTL_64_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_97_1

description:
Library name: 559-PTL_97_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_74_1

description:
Library name: 559-PTL_74_1
PTL_OS_clinical_data.xlsx


title: kidney biopsy N667


title: PTL_patient_128_1

description:
Library name: 559-PTL_128_1
PTL_OS_clinical_data.xlsx


title: Glucotonic_OLE-13-38-L004

description: Glucotonic_OLE_13 38_CAGATC_L004


title: PTL_patient_134_1

description:
Library name: 559-PTL_134_1
PTL_OS_clinical_data.xlsx


title: kidney biopsy N669


title: kidney biopsy N665


title: PTL_patient_131_1

description:
Library name: 559-PTL_131_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_127_1

description:
Library name: 559-PTL_127_1
PTL_OS_clinical_data.xlsx


title: kidney biopsy N663


title: PTL_patient_132_1

description:
Library name: 559-PTL_132_1
PTL_OS_clinical_data.xlsx


title: Sham_IL-15-30

source_name: ileum

value: ileum


title: PTL_patient_88_1

description:
Library name: 559-PTL_88_1
PTL_OS_clinical_data.xlsx


title: kidney biopsy N662


title: Sham_IL-14-28


title: kidney biopsy N659


title: kidney biopsy N660


title: kidney biopsy N666

value: pTCMR


title: Sham_IL-8-15


title: PTL_patient_50_1

description:
Library name: 559-PTL_50_1
PTL_OS_clinical_data.xlsx


title: kidney biopsy N664


title: PTL_patient_54_1

description:
Library name: 559-PTL_54_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_52_1

description:
Library name: 559-PTL_52_1
PTL_OS_clinical_data.xlsx


title: RYGB_CL-15-29

source_name: RYGB common limb

value: RYGB common limb


title: kidney biopsy N657


title: PTL_patient_46_1

description:
Library name: 559-PTL_46_1
PTL_OS_clinical_data.xlsx


title: RYGB_CL-2-3


title: PTL_patient_72_1

description:
Library name: 559-PTL_72_1
PTL_OS_clinical_data.xlsx


title: kidney biopsy N658


title: PTL_patient_130_1

description:
Library name: 559-PTL_130_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_98_1

description:
Library name: 559-PTL_98_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_92_1

description:
Library name: 559-PTL_92_1
PTL_OS_clinical_data.xlsx


title: kidney biopsy N661


title: PTL_patient_94_1

description:
Library name: 559-PTL_94_1
PTL_OS_clinical_data.xlsx


title: Sham_JEJU-15-30

source_name: jejunum

value: jejunum


title: RYGB_CL-1-1


title: kidney biopsy N653


title: Sham_JEJU-14-28


title: kidney biopsy N656


title: PTL_patient_26_1

description:
Library name: 559-PTL_26_1
PTL_OS_clinical_data.xlsx


title: RYGB_AL-15-29

source_name: RYGB alimentary limb

value: RYGB alimentary limb


title: PTL_patient_62_1

description:
Library name: 559-PTL_62_1
PTL_OS_clinical_data.xlsx


title: Sham_JEJU-8-15


title: PTL_patient_83_1

description:
Library name: 559-PTL_83_1
PTL_OS_clinical_data.xlsx


title: kidney biopsy N655


title: PTL_patient_79_1

description:
Library name: 559-PTL_79_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_77_1

description:
Library name: 559-PTL_77_1
PTL_OS_clinical_data.xlsx


title: kidney biopsy N654


title: RYGB_AL-2-3


title: PTL_patient_49_1

description:
Library name: 559-PTL_49_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_70_1

description:
Library name: 559-PTL_70_1
PTL_OS_clinical_data.xlsx


title: RYGB_AL-1-1


title: PTL_patient_55_1

description:
Library name: 559-PTL_55_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_85_1

description:
Library name: 559-PTL_85_1
PTL_OS_clinical_data.xlsx


title: 11D_time220_rep2

city: Barcelona

first: Montserrat

last: Vega

state: Barcelona

address: C/ Dr. Aiguader 88, lab 383

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra

description: Library name: Sample 78

data_processing:
Quality controls for FASTQ files using FastQC
Trim of low quality read bases from FASTQ files as well as removal of adapters and other contaminants using Trimmomatic
Alignment againts the Schizosaccharomyces pombe ASM294v2.48  genone reference using Star
Test for differentially expressed features between conditions using DESeq2
Assembly: Schizosaccharomyces pombe all chromosomes 20230315
Supplementary files format and content: tab-separated .txt table of DESeq2 normalized counts for all the samples

organism: Schizosaccharomyces pombe

source_name: S.pombe 11D mutant cells

growth_protocol: cdc25-22 cells carrying Nrm1-HA/Nrm1-SA-HA/Nrm1-SD-HA were grown in EMM at 25ºC until OD600=0.3  before blocking. Untreated cultures were separated until they reached OD600=0.5

extract_protocol:
Hot phenol extraction
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New Englar Biolabds)

treatment_protocol: cdc25-22 block and release. Cells block at 36ºC during 4 hours. Release at 25ºC. Samples every 20 minutes

value: S.pombe 11D mutant cells

value: cdc25-22 nrm1-SD-HA

value: block and release

tag: time point


title: PTL_patient_81_1

description:
Library name: 559-PTL_81_1
PTL_OS_clinical_data.xlsx

value: testicular lymphoma FFPE tissue


title: PTL_patient_86_1

description:
Library name: 559-PTL_86_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_90_1

description:
Library name: 559-PTL_90_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_51_1

description:
Library name: 559-PTL_51_1
PTL_OS_clinical_data.xlsx


title: kidney biopsy N652

value: Mixed


title: kidney biopsy N651

value: TCMR


title: 11D_time220_rep1

description: Library name: Sample 77


title: PTL_patient_47_1

description:
Library name: 559-PTL_47_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_104_1

description:
Library name: 560-PTL_104_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_101_1

description:
Library name: 560-PTL_101_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_73_1

description:
Library name: 559-PTL_73_1
PTL_OS_clinical_data.xlsx


title: 11D_time200_rep2

description: Library name: Sample 76


title: PTL_patient_109_1

description:
Library name: 560-PTL_109_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_122_1

description:
Library name: 560-PTL_122_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_29_1

description:
Library name: 560-PTL_29_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_102_1

description:
Library name: 560-PTL_102_1
PTL_OS_clinical_data.xlsx


title: 11D_time180_rep2

description: Library name: Sample 74


title: 11D_time180_rep1

description: Library name: Sample 73


title: PTL_patient_112_1

description:
Library name: 560-PTL_112_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_45_1

description:
Library name: 560-PTL_45_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_124_1

description:
Library name: 560-PTL_124_1
PTL_OS_clinical_data.xlsx


title: 11D_time160_rep2

description: Library name: Sample 72


title: 11D_time200_rep1

description: Library name: Sample 75


title: PTL_patient_121_1

description:
Library name: 560-PTL_121_1
PTL_OS_clinical_data.xlsx


title: 11D_time160_rep1

description: Library name: Sample 71


title: PTL_patient_28_1

description:
Library name: 560-PTL_28_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_118_1

description:
Library name: 560-PTL_118_1
PTL_OS_clinical_data.xlsx


title: 11D_time140_rep2

description: Library name: Sample 70


title: PTL_patient_111_1

description:
Library name: 560-PTL_111_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_34_1

description:
Library name: 560-PTL_34_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_39_1

description:
Library name: 560-PTL_39_1
PTL_OS_clinical_data.xlsx


title: 11D_time140_rep1

description: Library name: Sample 69


title: 11D_time120_rep2

description: Library name: Sample 68


title: PTL_patient_105_1

description:
Library name: 560-PTL_105_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_106_1

description:
Library name: 560-PTL_106_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_40_1

description:
Library name: 560-PTL_40_1
PTL_OS_clinical_data.xlsx


title: 11D_time120_rep1

description: Library name: Sample 67


title: PTL_patient_38_1

description:
Library name: 560-PTL_38_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_41_1

description:
Library name: 560-PTL_41_1
PTL_OS_clinical_data.xlsx


title: 11D_time100_rep2

description: Library name: Sample 66


title: PTL_patient_32_1

description:
Library name: 560-PTL_32_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_44_1

description:
Library name: 560-PTL_44_1
PTL_OS_clinical_data.xlsx


title: 11D_time100_rep1

description: Library name: Sample 65


title: PTL_patient_27_1

description:
Library name: 560-PTL_27_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_117_1

description:
Library name: 560-PTL_117_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_30_1

description:
Library name: 560-PTL_30_1
PTL_OS_clinical_data.xlsx


title: 11D_time80_rep2

description: Library name: Sample 64


title: PTL_patient_36_1

description:
Library name: 560-PTL_36_1
PTL_OS_clinical_data.xlsx


title: 11D_time80_rep1

description: Library name: Sample 63


title: PTL_patient_31_1

description:
Library name: 560-PTL_31_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_35_1

description:
Library name: 560-PTL_35_1
PTL_OS_clinical_data.xlsx


title: 11D_time60_rep2

description: Library name: Sample 62


title: PTL_patient_123_1

description:
Library name: 560-PTL_123_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_100_1

description:
Library name: 560-PTL_100_1
PTL_OS_clinical_data.xlsx


title: 11D_time60_rep1

description: Library name: Sample 61


title: PTL_patient_133_1

description:
Library name: 559-PTL_133_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_43_1

description:
Library name: 560-PTL_43_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_119_1

description:
Library name: 560-PTL_119_1
PTL_OS_clinical_data.xlsx


title: 11D_time40_rep2

description: Library name: Sample 60


title: PTL_patient_37_1

description:
Library name: 560-PTL_37_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_V_25_1

description:
Library name: 560-V_25_1
PTL_OS_clinical_data.xlsx


title: 11D_time40_rep1

description: Library name: Sample 59


title: PTL_patient_V_12_1

description:
Library name: 560-V_12_1
PTL_OS_clinical_data.xlsx


title: PTL_patient_P33_1

description:
Library name: 560-P33_1
PTL_OS_clinical_data.xlsx


title: 11D_time20_rep2

description: Library name: Sample 58


title: kidney biopsy N647

value: NR


title: kidney biopsy N649

value: ABMR


title: kidney biopsy N645


title: PTL_patient_Q8_1

description:
Library name: 367-Q8_1
PTL_OS_clinical_data.xlsx


title: 11D_time20_rep1

description: Library name: Sample 57


title: PTL_patient_P35_1

description:
Library name: 365-P35_1
PTL_OS_clinical_data.xlsx


title: kidney biopsy N646


title: PTL_patient_Q-11_1

description:
Library name: 365-Q-11_1
PTL_OS_clinical_data.xlsx


title: kidney biopsy N644


title: kidney biopsy N650


title: 11D_time0_rep2

description: Library name: Sample 56


title: PTL_patient_O23_1

description:
Library name: 362-O23_1
PTL_OS_clinical_data.xlsx


title: HEK293T_miR34a_rep3

city: Solna

first: Emma

middle: R

last: Andersson

address: Solnavägen 9

department: Department of Cell and Molecular Biology

country: Sweden

institute: Karolinska Institute

data_processing:
Reads were aligned to the human genome assembly version GRCh38 using STAR (version 2.7.11a).
Reads were assigned to genes using featureCounts in the subread package (version 2.0.3).
Differential gene expression analysis on the raw counts was carried out using edgeR (version 3.42.4).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file contains raw feature counts.

extract_protocol:
Total RNA was isolated with GeneJET RNA Purification Kit (Thermo Scientific, K0731). Samples were treated with Dnase I to clean up genomic DNA, followed by a second column purification using the GeneJET kit. The quality of the isolated RNA was checked on an Agilent 2100 BioAnalyzer with the RNA 6000 Nano Kit.
cDNA libraries were prepared with the TruSeq RNA Sample Preparation v2 kit (Illumina, RS-122-2001/RS-122-2002), according to the manufacturer's protocol.

value: transfected with miR-34a duplex


title: 11D_time0_rep1

description: Library name: Sample 55


title: HEK293T_miR34a_rep2


title: PTL_patient_R-27_1

description:
Library name: 364-R-27_1
PTL_OS_clinical_data.xlsx


title: 11D_as_rep2

description: Library name: Sample 54

value: untreated


title: HEK293T_AllStars_CTRL_rep3

value: transfected with AllStars negative control siRNA (Qiagen)


title: HEK293T_miR34a_rep1


title: kidney biopsy N648


title: HEK293T_AllStars_CTRL_rep2


title: 11D_as_rep1

description: Library name: Sample 53


title: kidney biopsy N636


title: kidney biopsy N639


title: Mko-3 cells, Huh-7 deficient in MTTP gene, biological replicate 3

city: Mineola

first: M. Mahmood

last: Hussain

state: New York

address: 101 Mineola Blvd.

department: Foundations of Medicine

institute: NYU Grossman Long Island School of Medicine

description: Library name: E3_KO

data_processing:
Raw data in fastq format were processed by Novogene using their in-house Perl scripts  to obtain clean reads by removing adapter sequences, reads with poly-N, and low-quality reads.
Trimmed sequence reads were mapped to GRCh37/hg19 using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg38
Supplementary files format and content: tab-limited text file includes raw counts for each sample
Supplementary files format and content: tab-limited text file includes FPKM values for each sample

growth_protocol: Mko-3 cells were grown and maintained in T75 flasks in DMEM with 10% fetal bovine serum (FBS) in humidified incubator with 5% CO2 at 37C.

extract_protocol:
Total RNA was isolated using Trizol reagent (Thermo Fisher Scientific, # 15596018) following manufacturers protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP. It was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: 80-90% confluent cells were washed three times with PBS and incubated overnight in serum free media

value: Human Hepatoma

value: MTTP knock out


title: kidney biopsy N626


title: kidney biopsy N635


title: kidney biopsy N629


title: kidney biopsy N637


title: kidney biopsy N627


title: kidney biopsy N642


title: kidney biopsy N638


title: 11A_time220_rep2

description: Library name: Sample 52

source_name: S.pombe 11A mutant cells

value: S.pombe 11A mutant cells

value: cdc25-22 nrm1-SA-HA


title: kidney biopsy N625


title: kidney biopsy N643


title: kidney biopsy N634


title: kidney biopsy N619


title: kidney biopsy N633


title: kidney biopsy N624


title: kidney biopsy N622

value: pABMR


title: Mko-3 cells, Huh-7 deficient in MTTP gene, biological replicate 2

description: Library name: E2_KO


title: kidney biopsy N632


title: kidney biopsy N641


title: kidney biopsy N623


title: kidney biopsy N631


title: Mko-3 cells, Huh-7 deficient in MTTP gene, biological replicate 1

description: Library name: E1_KO


title: MDA-MB-231 POLD1 Knockdown  1

city: New York

last: Possemato

state: NY

address: 550 First Avenue

department: Pathology

institute: NYU School of Medicine

description: Library name: MDA-MB-231 POLD1 Knockdown  1

data_processing:
Paired-end fastq files were trimmed using trimmomatic.
Trimmed reads were aligned with STAR to the Gencode GRCh38 genome reference file.
Read counts were generated using featureCounts with the Gencode v46 human GTF file.
Counts were then normalized to TPM (transcript-per-million) for visualization of expression. For differential expression, counts were normalized by DESeq2's median of ratios and analyzed using the DESeq2 package.
Assembly: GRCh38
Supplementary files format and content: CSV file, FPKM from samples in columns for genes indicated in first column

growth_protocol: RPMI 10% serum

extract_protocol:
RNeasy Plus Mini Kit, Automated stranded RNA-seq library prep, polyA selection
NovaSeq X Series 10B Reagent Kit

treatment_protocol: Cell lines transduced with shRNAs and expressingresistant cDNA (Control Knockdown) or vector control (Knockdown), 5d. Compound treatments: HU (2mM), Aph (2μg/mL), CP (12μM), CHX (2μM), PTX (4nM) or vehicle (NaCl or DMSO), 24 hrs.

value: Breast Cancer


title: 11A_time220_rep1

description: Library name: Sample 51


title: MDA-MB-231 POLD1 Control Knockdown  3

description: Library name: MDA-MB-231 POLD1 Control Knockdown  3


title: kidney biopsy N621


title: MDA-MB-231 POLD1 Knockdown  3

description: Library name: MDA-MB-231 POLD1 Knockdown  3


title: 11A_time200_rep1

description: Library name: Sample 49


title: kidney biopsy N630


title: MDA-MB-231 POLD1 Control Knockdown  2

description: Library name: MDA-MB-231 POLD1 Control Knockdown  2


title: kidney biopsy N628


title: kidney biopsy N640


title: kidney biopsy N620


title: MDA-MB-231 POLD1 Control Knockdown  1

description: Library name: MDA-MB-231 POLD1 Control Knockdown  1


title: 11A_time180_rep2

description: Library name: Sample 48


title: kidney biopsy N618


title: HEK293T_AllStars_CTRL_rep1


title: 11A_time180_rep1

description: Library name: Sample 47


title: MDA-MB-231 Taxol 2

description: Library name: MDA-MB-231 Taxol 2


title: MDA-MB-231 Taxol 1

description: Library name: MDA-MB-231 Taxol 1


title: kidney biopsy N617


title: MDA-MB-231 Taxol 3

description: Library name: MDA-MB-231 Taxol 3


title: MDA-MB-231 NaCl 3

description: Library name: MDA-MB-231 NaCl 3


title: kidney biopsy N615


title: 11A_time200_rep2

description: Library name: Sample 50


title: MDA-MB-231 POLD1 Knockdown  2

description: Library name: MDA-MB-231 POLD1 Knockdown  2


title: 11A_time160_rep2

description: Library name: Sample 46


title: kidney biopsy N616


title: MDA-MB-231 NaCl 2

description: Library name: MDA-MB-231 NaCl 2


title: MDA-MB-231 Hydroxyurea 3

description: Library name: MDA-MB-231 Hydroxyurea 3


title: kidney biopsy N613


title: MDA-MB-231 NaCl 1

description: Library name: MDA-MB-231 NaCl 1


title: 11A_time160_rep1

description: Library name: Sample 45


title: MDA-MB-231 Hydroxyurea 2

description: Library name: MDA-MB-231 Hydroxyurea 2


title: 11A_time140_rep2

description: Library name: Sample 44


title: MDA-MB-231 Hydroxyurea 1

description: Library name: MDA-MB-231 Hydroxyurea 1


title: kidney biopsy N612


title: kidney biopsy N614


title: MDA-MB-231 DMSO 3

description: Library name: MDA-MB-231 DMSO 3


title: kidney biopsy N610


title: 11A_time140_rep1

description: Library name: Sample 43


title: MDA-MB-231 DMSO 1

description: Library name: MDA-MB-231 DMSO 1


title: 11A_time120_rep1

description: Library name: Sample 41


title: 11A_time120_rep2

description: Library name: Sample 42


title: MDA-MB-231 Cisplatin 2

description: Library name: MDA-MB-231 Cisplatin 2


title: MDA-MB-231 Cisplatin 3

description: Library name: MDA-MB-231 Cisplatin 3


title: MDA-MB-231 DMSO 2

description: Library name: MDA-MB-231 DMSO 2


title: kidney biopsy N611


title: kidney biopsy N608


title: MDA-MB-231 Cycloheximide 3

description: Library name: MDA-MB-231 Cycloheximide 3


title: kidney biopsy N607


title: MDA-MB-231 Cycloheximide 1

description: Library name: MDA-MB-231 Cycloheximide 1


title: 11A_time100_rep1

description: Library name: Sample 39


title: kidney biopsy N606


title: MDA-MB-231 Aphidicolin 3

description: Library name: MDA-MB-231 Aphidicolin 3


title: MDA-MB-231 Aphidicolin 1

description: Library name: MDA-MB-231 Aphidicolin 1


title: MCF7 POLE Knockdown 3

description: Library name: MCF7 POLE Knockdown 3


title: MDA-MB-231 Aphidicolin 2

description: Library name: MDA-MB-231 Aphidicolin 2


title: 11A_time80_rep1

description: Library name: Sample 37


title: kidney biopsy N609


title: MDA-MB-231 Cisplatin 1

description: Library name: MDA-MB-231 Cisplatin 1


title: MCF7 POLE Knockdown 2

description: Library name: MCF7 POLE Knockdown 2


title: MCF7 Control Knockdown 3

description: Library name: MCF7 Control Knockdown 3


title: 11A_time60_rep1

description: Library name: Sample 35


title: MCF7 Control Knockdown 2

description: Library name: MCF7 Control Knockdown 2


title: 11A_time60_rep2

description: Library name: Sample 36


title: MCF7 POLE Knockdown 1

description: Library name: MCF7 POLE Knockdown 1


title: 11A_time100_rep2

description: Library name: Sample 40


title: MCF7 Control Knockdown 1

description: Library name: MCF7 Control Knockdown 1


title: MDA-MB-231 Cycloheximide 2

description: Library name: MDA-MB-231 Cycloheximide 2


title: Hs578T POLE Knockdown 2

description: Library name: Hs578T POLE Knockdown 2


title: kidney biopsy N594


title: 11A_time40_rep2

description: Library name: Sample 34


title: 11A_time80_rep2

description: Library name: Sample 38


title: Hs578T POLE Knockdown 3

description: Library name: Hs578T POLE Knockdown 3


title: kidney biopsy N604


title: Hs578T POLE Knockdown 1

description: Library name: Hs578T POLE Knockdown 1


title: 11A_time20_rep2

description: Library name: Sample 32


title: kidney biopsy N591


title: Hs578T Control Knockdown 1

description: Library name: Hs578T Control Knockdown 1


title: Hs578T Control Knockdown 2

description: Library name: Hs578T Control Knockdown 2


title: 11A_time20_rep1

description: Library name: Sample 31


title: MDA-MB-231 POLE Knockdown 3

description: Library name: MDA-MB-231 POLE Knockdown 3


title: MDA-MB-231 POLE Knockdown 2

description: Library name: MDA-MB-231 POLE Knockdown 2


title: MDA-MB-231 POLE Knockdown 1

description: Library name: MDA-MB-231 POLE Knockdown 1


title: MDA-MB-231 Control Knockdown 3

description: Library name: MDA-MB-231 Control Knockdown 3


title: 11A_time0_rep1

description: Library name: Sample 29


title: kidney biopsy N592


title: kidney biopsy N590


title: 11A_time0_rep2

description: Library name: Sample 30


title: kidney biopsy N598


title: kidney biopsy N587


title: kidney biopsy N589


title: MDA-MB-231 Control Knockdown 2

description: Library name: MDA-MB-231 Control Knockdown 2


title: kidney biopsy N585


title: 11A_as_rep1

description: Library name: Sample 27


title: 11A_time40_rep1

description: Library name: Sample 33


title: 11A_as_rep2

description: Library name: Sample 28


title: kidney biopsy N605


title: HUVEC MoesinWT bio rep2

city: TianJin

first: Lu

address: No22.Qixiangtai Rd.

country: China

institute: Tianjin medical university

description: Library name: L1HHD0700219--wt2

data_processing:
Raw FASTQ sequencing data was using kallisto for gene counting.
Assembly: hg38

source_name: endothelial cell

growth_protocol: Human Umbilical Vein Endothelial Cells (HUVECs) were cultured in Medium 199  supplemented with 10% fetal bovine serum, 4 µg/mL endothelial cell growth factor (ECGF), and 1% penicillin/streptomycin.Cells were maintained in a humidified incubator with 5% CO2 at 37 °C.

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’ s instructions.
RNA purification, reverse transcription, library construction and sequencing were performed according to the manufacturer’s instructions (Illumina, San Diego, CA). The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep Ligation from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly doublestranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, paired-end RNA-seq sequencing library was sequenced with the NovaSeqX plus sequencer (2 × 150bp read length).

treatment_protocol: Adenovirus infection

value: endothelial cell

value: infected with Ad-MoesinWT


title: Hs578T Control Knockdown 3

description: Library name: Hs578T Control Knockdown 3


title: HUVEC MoesinT558D bio rep2

description: Library name: L1HHD0700222--CA2

value: infected with Ad-MoesinT558D


title: HUVEC MoesinWT bio rep3

description: Library name: L1HHD0700220--wt3


title: WT_time220_rep1

description: Library name: Sample 25

source_name: S.pombe WT cells

value: S.pombe WT cells

value: cdc25-22 nrm1-HA

value: block and release


title: HUVEC MoesinT558D bio rep1

description: Library name: L1HHD0700221--CA1


title: HUVEC MoesinT558D bio rep3

description: Library name: L1HHD0700223--CA3


title: WT_time220_rep2

description: Library name: Sample 26


title: ae38_p1_sr1_1_S237

first: Yang

last: Lin

address: 455 Main Street 06W

institute: Weill Cornell Medicine

description:
Library name: Sample 71
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours

data_processing:
RNAseq
Paired-end reads were aligned to the human genome GRCh38 using the STAR aligner
Assembly: GRCh38
Supplementary files format and content: FPKM value of each gene from each sample. Excel file

source_name: Adipose

extract_protocol:
RNA was extracted with Rneasy Mini kit with on column DNAse treatment
TruSeq Stranded mRNA Library Preparation (Poly-A selection and Stranded RNA-Seq)

treatment_protocol: Cells were cultured in media contains 1: 10, 000 DMSO with or without 0.5uM SR1

value: Adipose

value: Endothelial cells

value: WT

tag: batch

value: Passage 1


title: AE38_P0_DMSO_1_S258

description:
Library name: Sample 69
Adipose EC treated with 1:10000 DMSO 48 hours

value: DMSO

value: Passage 0


title: AE34_SR1_P5_S251

description:
Library name: Sample 68
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours

value: Passage 5


title: ae38_p0_dmso_2_S259

description:
Library name: Sample 70
Adipose EC treated with 1:10000 DMSO 48 hours


title: AE38_P1_SR1_2_S248

description:
Library name: Sample 72
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours


title: HUVEC MoesinWT bio rep1

description: Library name: L1HHD0700218--wt1


title: kidney biopsy N584

address: 250 Heritage Medical Research Centre

institute: University of Alberta

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

value: ABMR


title: WT_time200_rep1

description: Library name: Sample 23


title: kidney biopsy N582


title: AE34_SR1_P4_S235

description:
Library name: Sample 67
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours

value: Passage 4


title: kidney biopsy N583

value: NR


title: kidney biopsy N581

value: pABMR


title: WT_time200_rep2

description: Library name: Sample 24


title: kidney biopsy N580


title: AE34_P3_DMSO_S255

description:
Library name: Sample 64
Adipose EC treated with 1:10000 DMSO 48 hours

value: Passage 3


title: WT_time180_rep1

description: Library name: Sample 21


title: kidney biopsy N579


title: WT_time160_rep2

description: Library name: Sample 20


title: WT_time180_rep2

description: Library name: Sample 22


title: AE34_P1_SR1_S234

description:
Library name: Sample 63
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours


title: AE34_P0_DMSO_S238

description:
Library name: Sample 61
Adipose EC treated with 1:10000 DMSO 48 hours


title: AE34_DMSO_P5_S214

description:
Library name: Sample 60
Adipose EC treated with 1:10000 DMSO 48 hours


title: AE34_P0_SR1_S233

description:
Library name: Sample 62
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours


title: WT_time140_rep2

description: Library name: Sample 18


title: AE34_DMSO_P2_S225

description:
Library name: Sample 58
Adipose EC treated with 1:10000 DMSO 48 hours

value: Passage 2


title: AE34_DMSO_P4_S244

description:
Library name: Sample 59
Adipose EC treated with 1:10000 DMSO 48 hours


title: kidney biopsy N572


title: WT_time140_rep1

description: Library name: Sample 17


title: AE32_SR1_P5_S246

description:
Library name: Sample 56
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours


title: AE32_SR1_P3_S222

description:
Library name: Sample 55
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours


title: AE34_SR1_P2_S226

description:
Library name: Sample 66
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours


title: AE34_P3_SR1_S257

description:
Library name: Sample 65
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours


title: AE32_SR1_P1_S231

description:
Library name: Sample 54
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours


title: WT_time120_rep2

description: Library name: Sample 16


title: kidney biopsy N578


title: kidney biopsy N355


title: AE32_P4_SR1_S240

description:
Library name: Sample 53
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours


title: AE32_P3_DMSO_S250

description:
Library name: Sample 52
Adipose EC treated with 1:10000 DMSO 48 hours


title: kidney biopsy N321


title: WT_time160_rep1

description: Library name: Sample 19


title: AE32_P2_SR1_S236

description:
Library name: Sample 51
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours


title: AE32_P1_SR1_S247

description:
Library name: Sample 50
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours


title: kidney biopsy N360


title: kidney biopsy N339


title: kidney biopsy N577

value: pTCMR


title: AE32_P0_SR1_S260

description:
Library name: Sample 48
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours


title: WT_time100_rep1

description: Library name: Sample 13

value: S.pombe WT cells


title: AE32_DMSO_P5_S249

description:
Library name: Sample 46
Adipose EC treated with 1:10000 DMSO 48 hours


title: WT_time80_rep2

description: Library name: Sample 12

value: cdc25-22 nrm1-HA


title: AE34_DMSO_P1_S230

description:
Library name: Sample 57
Adipose EC treated with 1:10000 DMSO 48 hours


title: kidney biopsy N382


title: AE32_DMSO_P2_S227

description:
Library name: Sample 44
Adipose EC treated with 1:10000 DMSO 48 hours


title: WT_time120_rep1

description: Library name: Sample 15

value: block and release


title: AE31_SR1_P5_S216

description:
Library name: Sample 43
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours

value: Adipose


title: kidney biopsy N390


title: AE32_P1_DMSO_S245

description:
Library name: Sample 49
Adipose EC treated with 1:10000 DMSO 48 hours

value: Endothelial cells


title: kidney biopsy N571

value: Mixed


title: AE31_SR1_P3_S223

description:
Library name: Sample 41
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours

value: WT


title: WT_time60_rep2

description: Library name: Sample 10


title: AE31_SR1_P2_S228

description:
Library name: Sample 40
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours


title: kidney biopsy N338


title: kidney biopsy N401

value: TCMR


title: AE31_SR1_P4_S219

description:
Library name: Sample 42
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours


title: AE31_P3_DMSO_S253

description:
Library name: Sample 38
Adipose EC treated with 1:10000 DMSO 48 hours

value: DMSO


title: AE31_SR1_P1_S232

description:
Library name: Sample 39
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours

value: Passage 1


title: kidney biopsy N586


title: AE32_P0_DMSO_S261

description:
Library name: Sample 47
Adipose EC treated with 1:10000 DMSO 48 hours

value: Passage 0


title: WT_time40_rep2

description: Library name: Sample 8


title: WT_time60_rep1

description: Library name: Sample 9


title: MDA-MB-231 Control Knockdown 1

description: Library name: MDA-MB-231 Control Knockdown 1

value: Breast Cancer


title: AE31_P2_DMSO_S241

description:
Library name: Sample 37
Adipose EC treated with 1:10000 DMSO 48 hours


title: kidney biopsy N320

value: ABMR


title: kidney biopsy N337

value: NR


title: kidney biopsy N381


title: AE31_DMSO_P5_S215

description:
Library name: Sample 36
Adipose EC treated with 1:10000 DMSO 48 hours

value: Passage 5


title: WT_time80_rep1

description: Library name: Sample 11


title: WT_time40_rep1

description: Library name: Sample 7


title: AE30_SR1_P5_S243

description:
Library name: Sample 34
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours


title: AE31_DMSO_P4_S218

description:
Library name: Sample 35
Adipose EC treated with 1:10000 DMSO 48 hours

value: Passage 4


title: AE30_SR1_P4_S221

description:
Library name: Sample 33
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours


title: WT_time20_rep2

description: Library name: Sample 6


title: WT_time20_rep1

description: Library name: Sample 5


title: AE30_P3_SR1_S239

description:
Library name: Sample 32
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours

value: Passage 3


title: AE30_P2_SR1_S256

description:
Library name: Sample 31
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours

value: Passage 2


title: kidney biopsy N319


title: kidney biopsy N405


title: kidney biopsy N404


title: kidney biopsy N570


title: WT_time0_rep2

description: Library name: Sample 4

value: S.pombe WT cells

value: cdc25-22 nrm1-HA


title: AE30_DMSO_P4_S220

description:
Library name: Sample 27
Adipose EC treated with 1:10000 DMSO 48 hours

value: Adipose


title: AE30_P1_SR1_S242

description:
Library name: Sample 30
Adipose EC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours

value: Endothelial cells


title: AE30_P1_DMSO_S254

description:
Library name: Sample 29
Adipose EC treated with 1:10000 DMSO 48 hours


title: AE30_DMSO_P3_S224

description:
Library name: Sample 26
Adipose EC treated with 1:10000 DMSO 48 hours


title: WT_as_rep2

description: Library name: Sample 2

value: untreated


title: AE30_DMSO_P5_S252

description:
Library name: Sample 28
Adipose EC treated with 1:10000 DMSO 48 hours

value: WT


title: RMR18_SR1_12h_S109

description:
Library name: Sample 23
HUVEC treated with 0.5uM SR1 in 1:10000 DMSO 12 hours

source_name: Umbilical Cord

value: Umbilical Cord


title: RMR18_DMSO_12h_S108

description:
Library name: Sample 21
HUVEC treated with 1:10000 DMSO 12 hours

value: DMSO


title: WT_time0_rep1

description: Library name: Sample 3

value: block and release


title: RMR04_SR1_48h_S119

description:
Library name: Sample 20
HUVEC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours


title: RMR18_DMSO_48h_S120

description:
Library name: Sample 22
HUVEC treated with 1:10000 DMSO 48 hours


title: RMR04_SR1_12h_S107

description:
Library name: Sample 19
HUVEC treated with 0.5uM SR1 in 1:10000 DMSO 12 hours


title: FL-96, Muscle, Female, Age-80

city: Geelong

first: Séverine

last: Lamon

state: VIC

address: 1 Gheringhap St

department: School of Exercise and Nutrition Sciences

country: Australia

institute: Deakin University

description:
Library name: FL-96
Column name in counts.csv: FL96_LION

data_processing:
Adapter trimming via Skewer (phred > 10)
Read alignment via Kallisto
Quality control monitoring via FastQC and MultiQC
Assembly: human transcriptome from Ensembl: GRCh38, release-111
Supplementary files format and content: csv text file includes raw counts for each sample

source_name: vastus lateralis muscle

extract_protocol:
TruSeq Stranded Total RNA Library Prep Gold Kit
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol and sequenced with 150-bp paired-end reads

value: vastus lateralis muscle

value: Female


title: FL-95, Muscle, Female, Age-47

description:
Library name: FL-95
Column name in counts.csv: FL95_RHSH


title: kidney biopsy N336

city: Edmonton

first: Jessica

last: Chang


title: FL-92, Muscle, Female, Age-75

description:
Library name: FL-92
Column name in counts.csv: FL92_JOOR


title: kidney biopsy N318

value: pABMR


title: kidney biopsy N568

value: NR


title: kidney biopsy N380


title: AE30_DMSO_P2_S229

description:
Library name: Sample 25
Adipose EC treated with 1:10000 DMSO 48 hours


title: kidney biopsy N398

value: ABMR


title: kidney biopsy N354


title: RMR18_SR1_48h_S121

description:
Library name: Sample 24
HUVEC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours


title: RMR04_DMSO_12h_S106

description:
Library name: Sample 17
HUVEC treated with 1:10000 DMSO 12 hours


title: WT_as_rep1

description: Library name: Sample 1


title: RMR02_DMSO_48h_S116

description:
Library name: Sample 14
HUVEC treated with 1:10000 DMSO 48 hours


title: RMR02_SR1_48h_S117

description:
Library name: Sample 16
HUVEC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours


title: RMR02_SR1_12h_S105

description:
Library name: Sample 15
HUVEC treated with 0.5uM SR1 in 1:10000 DMSO 12 hours


title: FL-91, Muscle, Female, Age-66

description:
Library name: FL-91
Column name in counts.csv: FL91_RABR


title: RMR02_DMSO_12h_S104

description:
Library name: Sample 13
HUVEC treated with 1:10000 DMSO 12 hours


title: RMR04_DMSO_48h_S118

description:
Library name: Sample 18
HUVEC treated with 1:10000 DMSO 48 hours


title: FL-89, Muscle, Female, Age-45

description:
Library name: FL-89
Column name in counts.csv: FL89_RALY


title: QH_SR1_48h_S123

description:
Library name: Sample 12
HUVEC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours

value: QH


title: QH_SR1_12h_S111

description:
Library name: Sample 11
HUVEC treated with 0.5uM SR1 in 1:10000 DMSO 12 hours


title: FL-85, Muscle, Female, Age-70

description:
Library name: FL-85
Column name in counts.csv: FL85_DAMA


title: QH_DMSO_48h_S122

description:
Library name: Sample 10
HUVEC treated with 1:10000 DMSO 48 hours


title: kidney biopsy N403


title: QH_DMSO_12h_S110

description:
Library name: Sample 9
HUVEC treated with 1:10000 DMSO 12 hours


title: FL-84, Muscle, Female, Age-72

description:
Library name: FL-84
Column name in counts.csv: FL84_JUHA


title: FL-82, Muscle, Female, Age-31

description:
Library name: FL-82
Column name in counts.csv: FL82_JULA


title: KM06_SR1_48h_S127

description:
Library name: Sample 8
HUVEC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours


title: KM06_SR1_12h_S115

description:
Library name: Sample 7
HUVEC treated with 0.5uM SR1 in 1:10000 DMSO 12 hours


title: kidney biopsy N559

value: TCMR


title: FL-79, Muscle, Female, Age-32

description:
Library name: FL-79
Column name in counts.csv: FL79_SAGE


title: KM06_DMSO_12h_S114

description:
Library name: Sample 5
HUVEC treated with 1:10000 DMSO 12 hours


title: kidney biopsy N558


title: KM06_DMSO_48h_S126

description:
Library name: Sample 6
HUVEC treated with 1:10000 DMSO 48 hours


title: KM02_SR1_48h_S125

description:
Library name: Sample 4
HUVEC treated with 0.5uM SR1 in 1:10000 DMSO 48 hours


title: FL-77, Muscle, Female, Age-55

description:
Library name: FL-77
Column name in counts.csv: FL77_CLRE


title: KM02_DMSO_48h_S124

description:
Library name: Sample 2
HUVEC treated with 1:10000 DMSO 48 hours


title: KM02_SR1_12h_S113

description:
Library name: Sample 3
HUVEC treated with 0.5uM SR1 in 1:10000 DMSO 12 hours


title: FL-78, Muscle, Female, Age-80

description:
Library name: FL-78
Column name in counts.csv: FL78_MAJA


title: KM02_DMSO_12h_S112

description:
Library name: Sample 1
HUVEC treated with 1:10000 DMSO 12 hours


title: FL-76, Muscle, Female, Age-74

description:
Library name: FL-76
Column name in counts.csv: FL76_LEGI


title: kidney biopsy N324


title: CTCs isolated from patient 025, sample 45

city: Zurich

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

description: Library name: p25_45

data_processing:
Trim Galore! (v0.6.6; parameters: –q 20 –length 20)
Quality assessment of RNA-seq data was carried out using FastQC (v0.11.9), FastQ Screen (v0.15.2), and visualized with MultiQC22 (v1.9)
Mapping using STAR (v 2.7.9) to human (GRCh38)  with splice junctions from the human GENCODE annotation (release 40)
Gene expression levels were computed with featureCounts from the subread package (v.2.0.3) using the human gene annotations from GENCODE (release 40)
Assembly: GRCh38 and GENCODE release 40
Supplementary files format and content: counts.txt.gz are tab-delimited files containing raw counts for each library

extract_protocol:
Blood samples were obtained via blood draw from multiple locations (via port, left brachiocephalic, superior vena cava, right atrium, portal vein, inferior vena cava, right iliac vein, left common iliac vein, aorta) in ACD-A vacutainers (Fisher Scientific, BD364606) and supplemented with 0.5 µg Tirofiban (Sigma-Aldrich, 30165) per ml of blood. Upon arrival, the samples were equilibrated at room temperature for 15 minutes. Subsequently, 7.5 µl of 0.5 M EDTA (Invitrogen, AM9260G) per ml of blood was added. The samples were then processed for microfluidic-based CTC capture within approximately 48 hours of the blood draw. Using the Parsortix Cell Separation System (ANGLE), CTCs were captured in Cell Separation cassettes (GEN3D6.5) and stained with an antibody cocktail containing anti-human EpCAM–AF488 (Cell Signaling Technology, CST5198), HER2–AF488 (BioLegend, 324410), EGFR–FITC (GeneTex, GTX11400), and CD45-AF647 (BioLegend, 304018).  The cDNA was processed using FLASH-seq protocol. After enrichment PCR, the samples were cleaned up with 0.8X AMPure Beads XP (Beckman Coulter, A63881) and the cDNA concentration was measured with the Tapestation and a High Sensitivity D5000 Screen Tape (Agilent).
Libraries were prepared using Nextera XT (Illumina) and sequenced on an Illumina NovaSeq X Plus instrumen.

value: ctc

tag: number of_cells

tag: patient id


title: CTCs isolated from patient 025, sample 47

description: Library name: p25_47


title: CTCs isolated from patient 025, sample 44

description: Library name: p25_44


title: CTCs isolated from patient 025, sample 43

description: Library name: p25_43


title: FL-74, Muscle, Female, Age-77

description:
Library name: FL-74
Column name in counts.csv: FL74_ZADU


title: kidney biopsy N556


title: kidney biopsy N555


title: FL-73, Muscle, Female, Age-75

description:
Library name: FL-73
Column name in counts.csv: FL73_JUCA


title: CTCs isolated from patient 025, sample 38

description: Library name: p25_38


title: CTCs isolated from patient 025, sample 34

description: Library name: p25_34


title: FL-72, Muscle, Female, Age-36

description:
Library name: FL-72
Column name in counts.csv: FL72_COVA


title: CTCs isolated from patient 022, sample 15

description: Library name: TP22_PCa15


title: CTCs isolated from patient 025, sample 27

description: Library name: p25_27


title: kidney biopsy N323


title: CTCs isolated from patient 022, sample 10

description: Library name: TP22_PCa10


title: FL-71, Muscle, Female, Age-49

description:
Library name: FL-71
Column name in counts.csv: FL71_KYSM


title: CTCs isolated from patient 022, sample 1

description: Library name: TP22_PCa1


title: FL-70, Muscle, Female, Age-55

description:
Library name: FL-70
Column name in counts.csv: FL70_COST


title: FL-67, Muscle, Female, Age-33

description:
Library name: FL-67
Column name in counts.csv: FL67_KALE


title: kidney biopsy N557


title: CTCs isolated from patient 021, sample 6

description: Library name: P021_6


title: kidney biopsy N548


title: kidney biopsy N552


title: kidney biopsy N553


title: kidney biopsy N551


title: FL-66, Muscle, Female, Age-19

description:
Library name: FL-66
Column name in counts.csv: FL66_MECA


title: kidney biopsy N549


title: kidney biopsy N550


title: CTCs isolated from patient 037, sample 1

description: Library name: P037_1


title: FL-63, Muscle, Female, Age-58

description:
Library name: FL-63
Column name in counts.csv: FL63_VALO


title: kidney biopsy N547


title: CTCs isolated from patient 011, sample 14

description: Library name: p11_14


title: CTCs isolated from patient 012, sample 2

description: Library name: SA_T12_PM_2_tri


title: CTCs isolated from patient 021, sample 8

description: Library name: P021_8


title: FL-62, Muscle, Female, Age-59

description:
Library name: FL-62
Column name in counts.csv: FL62_RINA


title: CTCs isolated from patient 011, sample 13

description: Library name: p11_13


title: CTCs isolated from patient 011, sample 9

description: Library name: p11_9


title: CTCs isolated from patient 021, sample 3

description: Library name: P021_3


title: FL-61, Muscle, Female, Age-24

description:
Library name: FL-61
Column name in counts.csv: FL61_SOMA


title: CTCs isolated from patient 021, sample 1

description: Library name: P021_1


title: WT_time100_rep2

description: Library name: Sample 14

value: S.pombe WT cells


title: CTCs isolated from patient 012, sample 3

description: Library name: SA_T12PM_3

source_name: cto

value: cto


title: kidney biopsy N541

source_name: kidney biopsy


title: CTCs isolated from patient 011, sample 8

description: Library name: p11_8


title: kidney biopsy N379


title: CTCs isolated from patient 011, sample 7

description: Library name: p11_7


title: FL-58, Muscle, Female, Age-68

description:
Library name: FL-58
Column name in counts.csv: FL58_ANKE


title: CTCs isolated from patient 011, sample 6

description: Library name: p11_6


title: CTCs isolated from patient 010, sample 15

description: Library name: Pat10_15


title: FL-56, Muscle, Female, Age-47

description:
Library name: FL-56
Column name in counts.csv: FL56_JARU


title: CTCs isolated from patient 010, sample 9

description: Library name: Pat10_9


title: CTCs isolated from patient 010, sample 6

description: Library name: SA_T10PM_6


title: kidney biopsy N542


title: AE32_DMSO_P4_S217

description:
Library name: Sample 45
Adipose EC treated with 1:10000 DMSO 48 hours

value: Adipose

value: Passage 4


title: FL-55, Muscle, Female, Age-53

description:
Library name: FL-55
Column name in counts.csv: FL55_LYRI


title: CTCs isolated from patient 010, sample 1

description: Library name: SA_T10_PM_1_resequenced


title: CTCs isolated from patient 010, sample 11

description: Library name: SA_T10PM_11


title: HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:1, replicate3

city: Aurora

first: Christopher

last: Ng

state: Colorado

address: 12800 East 19th Ave

institute: University of Colorado - Anschutz Medical Campus

description:
Library name: D1V60F3
HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:1

data_processing:
Each sample had 10M reading pairs per 20M total reads. RNA-seq analysis was conducted using Salmon and edgeR-based quantification to generate raw counts and CPM matrices
Assembly: GrCh38
Supplementary files format and content: Salmon Quantification Exports, (.sf) files.

source_name: HUVEC

growth_protocol: Human umbilical vein cells (HUVECs), Human Pulmonary Artery Endothelial Cells (HPAEC), and Human Lung Microvascular Endothelial Cells (HMVEC) primary cells were purchased from Lonza (Portsmouth, NH). All endothelial cells used for experimentation were passaged no more than 7 time. Endothelial cells were sustained in EBM2-MV (Lonza) supplemented with 10% fetal Bovine serum (FBS). Experiments were orchestrated to ensure similar passage across cell lines.

extract_protocol:
After relevant experimentation, RNA was extracted using miRNeasy Mini Kit and direct cellular lysis in the slide
The Universal Plus mRNA-Seq library preparation kit with NuQuant was used (Tecan) with an input of 200ng of total RNA to generate RNA-Seq libraries

treatment_protocol: Cells were harvested and reseeded into a µ-Slide I Luer (IBIDI 80166) at density of 60,000 cells/cm2 or 100,000 cells/cm2.  After 24hr, the cells were washed with PBS and a total of 120µL of fresh medium was added to the cells. For control samples, the slide was placed back in the incubator and medium was changed every 24 hours until the conclusion of the experiment. For flow samples, the slide was connected to 100cm of tubing on each end of the slide. 0.5mm diameter tubing was used to create the 1dynes/cm2 flow condition, 0.8mm dimeter tubing was used to create the 4dynes/cm2 flow condition, and 1.6mm diameter tubing to create the 10 dynes/cm2 flow condition. One end of the tubing was then connected to a reservoir of medium that was kept inside of the incubator with the slide and the other end of the tubing was connected to a syringe outside of the incubator. The syringe was then attached to the Standard Infuse/Withdraw PHD ULTRA™ Syringe Pumps (Harvard Apparatus 70-3007). The desired flow rate was input into the device and flow was started. Flow was applied to the cells for a total of 24 or 48 hours and every 22 minutes the direction of flow was changed from infuse to withdraw.

value: HUVEC

value: commercial endothelial cells

value: Time:48hrs, Seeding density (cells/cm2):60,000, Dynes:1


title: kidney biopsy N378


title: FL-53, Muscle, Female, Age-58

description:
Library name: FL-53
Column name in counts.csv: FL53_COKI


title: FL-52, Muscle, Female, Age-36

description:
Library name: FL-52
Column name in counts.csv: FL52_RUCH


title: kidney biopsy N540


title: HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:1, replicate2

description:
Library name: D1V60F2
HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:1

value: WT


title: kidney biopsy N377


title: kidney biopsy N317


title: HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:1, replicate1

description:
Library name: D1V60F1
HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:1


title: FL-50, Muscle, Female, Age-47

description:
Library name: FL-50
Column name in counts.csv: FL50_IRCH


title: HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate9

description:
Library name: D1V60C2
HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0

value: Time:48hrs, Seeding density (cells/cm2):60,000, Dynes:0


title: FL-5, Muscle, Female, Age-61

description:
Library name: FL-5
Column name in counts.csv: FL5_RURY

value: vastus lateralis muscle


title: kidney biopsy N539

value: Mixed


title: HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate10

description:
Library name: D1V60C3
HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:1, replicate3

description:
Library name: D1A60F3
HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:1

source_name: HPAEC

value: HPAEC


title: kidney biopsy N546

value: NR


title: HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:1, replicate1

description:
Library name: D1A60F1
HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:1


title: FL-47, Muscle, Female, Age-37

description:
Library name: FL-47
Column name in counts.csv: FL47_JUGR

value: Female


title: FL-49, Muscle, Female, Age-47

description:
Library name: FL-49
Column name in counts.csv: FL49_TRVA


title: HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate8

description:
Library name: D1V60C1
HUVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: kidney biopsy N538


title: HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:1, replicate2

description:
Library name: D1A60F2
HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:1


title: kidney biopsy N536

value: ABMR


title: HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate10

description:
Library name: D1A60C1
HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: CTCs isolated from patient 022, sample 6

description: Library name: TP22_PCa6


title: kidney biopsy N537


title: HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate11

description:
Library name: D1A60C2
HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: kidney biopsy N535


title: HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate12

description:
Library name: D1A60C3
HPAEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: FL-46, Muscle, Female, Age-27

description:
Library name: FL-46
Column name in counts.csv: FL46_MEEM


title: HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:1, replicate3

description:
Library name: D1M60F3
HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:1

source_name: HMVEC

value: HMVEC


title: FL-45, Muscle, Female, Age-19

description:
Library name: FL-45
Column name in counts.csv: FL45_CICA


title: HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate10

description:
Library name: D1M60C3
HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: kidney biopsy N534


title: HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:1, replicate1

description:
Library name: D1M60F1
HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:1


title: FL-44, Muscle, Female, Age-28

description:
Library name: FL-44
Column name in counts.csv: FL44_HEBA


title: HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate9

description:
Library name: D1M60C2
HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: HepKD3

city: Jinan

first: Rui zhe

last: Li

address: No.104, Wen hua west Road

institute: Shandong University

description: Library name: Sample12

data_processing:
CLC Genomics Workbench v 11.0.1.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit: 0.05).
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: GRCh38.p14 (GCA_000001405.29)
Supplementary files format and content: Excel .xlsx files include raw counts and TPM values.

extract_protocol:
RNA was harvested using RNAfast-2000 kit (Fastagen). 1.3 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: hepatocellular carcinoma cell

tag: condition

value: Hypoxia


title: HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0, replicate8

description:
Library name: D1M60C1
HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:0


title: FL-43, Muscle, Female, Age-52

description:
Library name: FL-43
Column name in counts.csv: FL43_CACA


title: HepKD2

description: Library name: Sample11


title: FL-42, Muscle, Female, Age-29

description:
Library name: FL-42
Column name in counts.csv: FL42_ANLE


title: HepKD1

description: Library name: Sample10


title: kidney biopsy N533


title: kidney biopsy N531

value: TCMR


title: FL-41, Muscle, Female, Age-20

description:
Library name: FL-41
Column name in counts.csv: FL41_NAWO


title: HepNC3

description: Library name: Sample9

value: shNC


title: HepNC2

description: Library name: Sample8


title: H7KD3

description: Library name: Sample6


title: kidney biopsy N530


title: HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:1, replicate2

description:
Library name: D1M60F2
HMVEC,Time: 48hrs, Seeding density (cells/cm2): 60,000, Dynes:1


title: FL-40, Muscle, Female, Age-62

description:
Library name: FL-40
Column name in counts.csv: FL40_SAVA


title: H7KD2

description: Library name: Sample5


title: kidney biopsy N529


title: FL-39, Muscle, Female, Age-30

description:
Library name: FL-39
Column name in counts.csv: FL39_HECH


title: H7KD1

description: Library name: Sample4


title: FL-38, Muscle, Female, Age-35

description:
Library name: FL-38
Column name in counts.csv: FL38_ERMA


title: H7NC3

description: Library name: Sample3


title: H7NC2

description: Library name: Sample2


title: kidney biopsy N532


title: FL-35, Muscle, Female, Age-19

description:
Library name: FL-35
Column name in counts.csv: FL35_ARDA


title: kidney biopsy N527


title: kidney biopsy N528


title: KDM6A-KD,skin fibroblasts,KDM6B (ChIP)

city: Shanghai

first: Jun

last: Mi

address: 280 South Chongqing Rd.

department: Biochemistry & Molecular Cell Biology

institute: Shanghai Jiao Tong University

description: Library name: KDM6A_KD,ChIP

data_processing:
Quality control for the raw sequencing data were performed by using fastqc v0.11.9 and cutadapt v3.4 to remove adapter sequences and low-quality sequences. Then, the clean reads were mapped to the human genome (hg38) using bowtie2 v2.2.4 with default parameters, and only uniquely and properly paired mapping reads were retained. The resultant BAM files were converted into bigWig files using bamCoverage tool from deepTools version 3.5.1 with parameters (--normalizeUsing RPGC; --binSize 100; --smoothLength 200).
Assembly: hg38
Supplementary files format and content: BigWig, narrow peak

source_name: Skin tissue

growth_protocol: DMEM, 15% fetal bovine serum, 1× penicllin/streptomycin.Cells were cultured at 37℃ at 5%CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. Then the steps were followed using Simple ChiP Plus Sonication Chromatin IP Kit (56383, Cell Signaling Technology) according to manufacturer’s instructions. ChIP-seq of KDM6B in the fibroblasts depleted of KDM6A.
Add "A" to the DNA sample after immunoprecipitation according to the kit for end repair; The product was purified by magnetic beads; The linker ligation reaction was configured, followed by purification and fragment sorting with magnetic beads; The PCR reaction system was configured and the reaction program was set to amplify the ligated products; The amplified PCR product was purified by magnetic beads to recover the target fragment, and the purified library was dissolved in elution buffer.

value: Skin tissue

value: Primary cell

value: Human fibroblast


title: Ctrl,skin fibroblasts,KDM6B (ChIP)

description: Library name: Ctrl,ChIP

value: ctrl


title: kidney biopsy N526


title: HepNC1

description: Library name: Sample7


title: KDM6A_KD, skin fibroblasts (Input)

description: Library name: KDM6A_KD, Input


title: FL-33, Muscle, Female, Age-23

description:
Library name: FL-33
Column name in counts.csv: FL33_HEMY


title: kidney biopsy N525


title: Ako-3 cells, Huh-7 deficient in APOBgene, biological replicate 3

growth_protocol: Huh-7 and Ako-3 cells were grown and maintained in T75 flasks in DMEM with 10% fetal bovine serum (FBS) in humidified incubator with 5% CO2 at 37C.

value: Human Hepatoma

value: APOB knock out


title: Ako-3 cells, Huh-7 deficient in APOBgene, biological replicate 2


title: kidney biopsy N524


title: FL-32, Muscle, Female, Age-68

description:
Library name: FL-32
Column name in counts.csv: FL32_JASY

value: vastus lateralis muscle


title: FL-30, Muscle, Female, Age-64

description:
Library name: FL-30
Column name in counts.csv: FL30_SAKE


title: H7NC1

description: Library name: Sample1


title: Huh-7 cells, Biological replicate 2

value: WT


title: kidney biopsy N523

value: pABMR


title: Huh-7 cells, Biological replicate 1


title: kidney biopsy N522


title: FL-28, Muscle, Female, Age-28

description:
Library name: FL-28
Column name in counts.csv: FL28_ANCH


title: FL-27, Muscle, Female, Age-28

description:
Library name: FL-27
Column name in counts.csv: FL27_ELBE


title: kidney biopsy N521

value: Mixed


title: FL-34, Muscle, Female, Age-25

description:
Library name: FL-34
Column name in counts.csv: FL34_GUNY

value: Female


title: Ctrl, skin fibroblasts (Input)

description: Library name: Ctrl, Input


title: kidney biopsy N520

value: ABMR


title: kidney biopsy N519


title: FL-21, Muscle, Female, Age-67

description:
Library name: FL-21
Column name in counts.csv: FL21_ANCO


title: FL-20, Muscle, Female, Age-30

description:
Library name: FL-20
Column name in counts.csv: FL20_ELGA


title: FL-18, Muscle, Female, Age-59

description:
Library name: FL-18
Column name in counts.csv: FL18_SUMO


title: Ako-3 cells, Huh-7 deficient in APOBgene, biological replicate 1


title: Huh-7 cells, Biological replicate 3


title: Zea mays B73, primary and seminal root tip (0-1mm), Nuclear RNA-seq, biorep5

city: Raleigh

first: Linda

last: Hanley-Bowdoin

state: NC

address: 851 Main Campus Drive, Partners III Suite 360

department: Plant and Microbial Biology

institute: North Carolina State University

description: Total nuclear RNA without biotin-streptavidin pulldown

data_processing:
Adapter trimming (trimmomatic-0.36 PE -phred33 -validatePairs ILLUMINACLIP:/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa:2:30:10:2:True LEADING:5 TRAILING:5 MINLEN:20)
Contaminants filtration (sortmerna -ref contaminants.fasta -reads $SAMPLE.input.fw.fastq -reads $SAMPLE.input.rv.fastq --out2 True --kvdb $SAMPLE.kvdb --readb $SAMPLE.readb --idx-dir sortmerna.idx-dir --zip-out Yes --fastx true --blast '1 cigar qcov qstrand' --paired_in true --other $SAMPLE.processed)
Read mapping (STAR --genomeDir STAR_2.7.10b.GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0 --outSAMtype BAM SortedByCoordinate --outMultimapperOrder Random --outFilterMultimapNmax 1 --readFilesIn $SAMPLE.fw.fastq $SAMPLE.rv.fastq --outFileNamePrefix $SAMPLE.mapped)
Alignments filtering (samtools view -bh -f 0x2 $SAMPLE.bam)
Alignments deduplication (umi_tools dedup -I $SAMPLE.bam -S $SAMPLE.deduplicated.bam --umi-separator=":" --paired )
Genomic coverage (bamCoverage --binSize 50 --normalizeUsing RPGC --effectiveGenomeSize 2209328549 --outFileFormat bigwig --filterRNAstrand forward --bam $SAMPLE.deduplicated.bam --outFileName $SAMPLE.deduplicated.fw.bw )
Read count (htseq-count -f bam --order=pos --stranded=reverse -a 0 -t exon -i gene --nonunique=fraction --mode=union --counts_output=$SAMPLE.counts.tsv $SAMPLE.deduplicated.bam Zm-B73-REFERENCE-NAM-5.0_genomic.with_scaffolds.GENE.coding+non_coding+pseudo.EXONS.gff)
Assembly: GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.fasta
Supplementary files format and content: bigwig files with read density coverage
Supplementary files format and content: tables with raw read counts

molecule: nuclear RNA

organism: Zea mays

source_name: Terminal 1 mm of primary and seminal roots

growth_protocol: B73 seeds were imbibed overnight with stirring and aeration, and the next day surface sterilized with 10% commercial bleach; 0.05% Tween 20 solution for 15 min at room temperature, rinsed 4X with sterile water and germinated in sterilized magenta boxes with paper towels dampened with sterile water. Seedlings were grown in a growth chamber at 28 C for 3 days under continuous dim fluorescent light (~500 lux).

extract_protocol:
Nuclear RNA was isolated using the Qiagen RNeasy FFPE Kit (ref # 73504). The kit is designed to purify RNA from fixed, paraffin-embedded tissue sections. We skipped the deparaffinization steps and began the protocol at step six of the handbook. Nuclear RNAs were DNAase treated with the Invitrogen Turbo DNA-free kit and ribosomal RNAs were removed with the Vazyme Ribo-off rRNA depletion kit for plants.
NEBNext Ultra II Directional RNA Library kit for Illumina with NEBNext Multiplex Oligos for Illumina, Unique Dual Index UMI Adaptors RNA set 1.

treatment_protocol: Conditioned for 1 hr in water then labeled for 1 hr in 175 uM 5-ethynyl uridine.

tag: developmental stage

value: seedling primary and seminal root meristem region

tag: cultivar

value: 3-days after germination

value: conditioned for 1 hr in water then labeled for 1 hr in 175 uM 5-ethynyl uridine


title: Zea mays B73, primary and seminal root tip (0-1mm), Nuclear RNA-seq, biorep4

tag: tissue

value: Terminal 1 mm of primary and seminal roots

tag: treatment


title: kidney biopsy N515


title: FL-29, Muscle, Female, Age-21

description:
Library name: FL-29
Column name in counts.csv: FL29_CAPE


title: Zea mays B73, primary and seminal root tip (0-1mm), Nuclear RNA-seq, biorep3


title: kidney biopsy N513


title: kidney biopsy N512

value: NR


title: FL-15, Muscle, Female, Age-31

description:
Library name: FL-15
Column name in counts.csv: FL15_JOSC


title: Zea mays B73, primary and seminal root tip (0-1mm), Nuclear RNA-seq, biorep2


title: FL-14, Muscle, Female, Age-40

description:
Library name: FL-14
Column name in counts.csv: FL14_KAWY


title: kidney biopsy N516


title: kidney biopsy N517


title: kidney biopsy N514


title: Zea mays B73, primary and seminal root tip (0-1mm), Nuclear RNA-seq, biorep1


title: FL-24, Muscle, Female, Age-21

description:
Library name: FL-24
Column name in counts.csv: FL24_LAMC


title: Zea mays B73, primary and seminal root tip (0-1mm), Nuclear EU nascent RNA-seq, biorep5

description: EU-nuclear RNA from biotin-streptavidin pulldown


title: FL-17, Muscle, Female, Age-26

description:
Library name: FL-17
Column name in counts.csv: FL17_EMHO


title: FL-13, Muscle, Female, Age-44

description:
Library name: FL-13
Column name in counts.csv: FL13_ANCL


title: Zea mays B73, primary and seminal root tip (0-1mm), Nuclear EU nascent RNA-seq, biorep4


title: FL-11, Muscle, Female, Age-61

description:
Library name: FL-11
Column name in counts.csv: FL11_ANSH


title: Zea mays B73, primary and seminal root tip (0-1mm), Nuclear EU nascent RNA-seq, biorep3


title: FL-1, Muscle, Female, Age-33

description:
Library name: FL-1
Column name in counts.csv: FL1_DAHI


title: Zea mays B73, primary and seminal root tip (0-1mm), Nuclear EU nascent RNA-seq, biorep2