title: LCC9, biological rep1 [lncRNA and mRNA]

description:
FUL-3
LncRNA and mRNA expression data from LCC9 cells.


title: FNE 2

status: Public on Nov 18 2020

type: SRA

city: Princeton

first: Wei

last: Wang

state: NJ

address: 135 Icahn Lab

country: USA

institute: Princeton University

library_source: transcriptomic

data_processing:
The HyperTRIBE protocol (described here: https://github.com/rosbashlab/HyperTRIBE/blob/5fd64d45eca926923e76825cb2e86f342206bfbf/docs/source/run.rst) was used, following the RNA-to-RNA pipeline. All scripts edits and parameters were performed as described in the documentation. The steps are briefly described below
RefSeq Curated Genes and Gene Predictions for dm6 were downloaded using the UCSC Table Browser and converted to refflat format to be supplied to HyperTRIBE.  GTF annotations and fasta sequence were also downloaded from UCSC to be supplied to STAR
Reads were trimmed using Trimmomatics (version 0.36) and aligned using STAR (version 2.7.3a)
The alignments were recorded in SAM format (samtools version 1.10), which were then loaded into MySQL (MySQL version 15.1, build 5.5.64-MariaDB (Linux (x86_64) using readline 5.1))
A Perl (version 5.10.1) script was run to compare each sample to WT RNA to identify RNA editing events and identify editing sites that met the following thresholds (5% editing, 20 reads)
Genome_build: dm6
Supplementary_files_format_and_content: bedgraph files with peaks indicating editing sites (bedtools version 2.29.0)

molecule: total RNA

organism: Drosophila melanogaster

source_name: Schneider S2 cells

growth_protocol: Drosophila S2 cells grown at 25C in culture flasks

extract_protocol:
Cells were harvested and resuspended in lysis buffer (10mM Tris HCl pH 7.5, 150 mM NaCl, 0.5 mM EDTA, 0.5% NP-40). Samples were treated with RQ1 DNase and RNA was extracted using TRIzol reagent.
Illumina sequencing libraries were prepared using the PrepX RNA-seq protocol on the automated Apollo 324TM NGS Library Prep System (TakaraBio, CA).

treatment_protocol: Cells were treated with CuSO4 for 24 h to induce expression of either Fne-ADAR or ADAR

tag: treatment

value: 24 h CuSO4

tag: cell line

tag: genotype

value: FNE-ADAR


title: ADAR 2

value: ADAR


title: FNE 1


title: WT RNA

value: WT


title: ADAR 1


title: Human epicardial EV (Cobble) 2

city: Madrid

first: Cristina

middle: Villa

last: del Campo

state: Madrid

address: Melchor Fernandez Almagro, 3 Pabellon 18, CNIC

country: Spain

institute: CNIC

description:
p222sC2_Cristina_S70_L008
Human cobble epic EV

data_processing:
Sequence reads were pre-processed to remove adapters and retain only 16-30 base pair- length reads
The reads aligning to each known mature miRNA were counted using Bioconductor packages for next-generation sequencing data analysis based on miRNA definitions in miRBase database
The differential expression analysis between different sample types was performed using the negative binomial statistical model of read counts as implemented in the DESeqBioconductor package
The statistical significance of differential expression is established based on the FDR-adjusted p-values. The cluster analysis of all differentially expressed miRNA was performed using the Bayesian infinite mixture model. Pathway enrichment analysis was conducted with Gene Ontology (GO)
Enrichment p-values were corrected for false discovery rate (FDR) and were considered significant when adjusted p ≤ 0.05.
Supplementary_files_format_and_content: Counts for miRNAs

organism: Homo sapiens

source_name: Evs from human epicardial cells (cobble)

growth_protocol: Cells were grown in standard culture conditions

extract_protocol:
AllPrep DNA/RNA Mini Kit
Library preparation was performed using TrueSeq Kit (TruSeq Small RNA Library Prep Kit Illumina Cat N° RS-200-0012) with modifications on gel size selection (30-300bp fragments).

tag: cell type

value: human epicardial cells (cobble)

tag: sample type

value: extracellular vesicles (Evs)

tag: molecule subtype

value: miRNA


title: Lmna-/- 7

city: Houaton

first: Ali

middle: J

last: Marian

state: Texas

address: 6770 Bertner Ave DAC C900a

department: Centre for Cardiovascular Genetics

institute: UTHSC, Houston

data_processing:
Mapping of sequencing reads to the mouse genome GRCm38.91 (Ensembl) was performed using Tophat2  using mm10 mouse genome as reference.
Read quantitation on a per-gene basis was performed with HTSeq  and the default gene annotation file (gtf) provided with the GRCm38.91 Ensembl genome distribution. Calculation of fold-change and FDR for differentially expressed RNAs used the R/Bioconductor packages limma and edgeR/voom.A batch correction was performed through by including batch as a blocking factor in the linear model used by limma.
Differential gene expression was determined using EdgeR.
Supplementary_files_format_and_content: xlsx file contains the cpm for the Samples and the calculated log2ratio for the KO and AAV9 samples  along with the FDR and pvalue for the comparison.

organism: Mus musculus

source_name: Heart

extract_protocol:
A miRNeasy Mini Kit  (Qiagen, Cat:217004) was used to isolate the RNA following the manufacturer's guidelines
A Illumina TruSeq kit was used in library preparation following the manufacturer's guidelines.

tag: tissue

value: Heart

tag: strain

value: Mixed

tag: age

value: 2 week

value: Lmna knockout


title: Human epicardial EV (Cobble) 1

description:
p222sC1_Cristina_S69_L008
Human cobble epic EV


title: mepic EV 1

description:
p312sMedicExD1_Zimmermann_S46_L006
Medic ExD1
the processed data file contains miRNAs counts present in the mouse epicardial Evs. Combination of two sequencing runs (mepic EV 1 and mepic EV 2 samples, available in the mepic EV 1 sample records )

source_name: Evs from mouse epicardial cells

value: mouse epicardial cells


title: 10007599-1

city: Rochester

first: Xiaojia

last: Tang

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina CASAVA 1.9 pipeline
QC was performed on the FASTQ files using fastQC
Alignment and gene counts were obtained through MAPR-Seq pipeline v2.0.
Genome_build: hg19
Supplementary_files_format_and_content: GeneCount_raw.txt

source_name: Tissue Biopsy

extract_protocol:
Biopsy samples were thawed on ice, homogenized, and centrifuged at 13,000 RPM, and the supernatant was transferred to a new tube.
RNA was prepared using the RNeasy Mini Kit (QIAGEN, Hilden, Germany).

tag: patientid

tag: timepoint

tag: bmi

tag: gender

value: M

tag: cohort

value: Healthy


title: 10007611-2

value: F

value: Constipation


title: Human epicardial EV (Spindle) 1

description:
p222sS1_Cristina_S71_L008
Human spindle epic EV

source_name: Evs from human epicardial cells (spindle)

value: human epicardial cells (spindle)


title: 10007605-1


title: 10007587-1


title: 10007594-2

value: Diarrhea


title: 10007572-2


title: 10007569-1


title: 10007587-2


title: 10007578-2


title: 10007578-1


title: 10007569-2


title: 10007544-2


title: 10007567-2


title: siPTBP1+siPTBP2 CH Replicate 3

city: LOS ANGELES

first: Chia-ho

last: Lin

state: CA

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

description: siPTBP1+siPTBP2 CH Replicate 3

data_processing:
Sequencing reads were mapped to the mm10 genome using STAR. Intron retention analysis was conducted using SQUID that was developed from the Xing lab.
gene expression estimation with Kallisto
Genome_build: mm10

source_name: E14 mESCs

growth_protocol: E14 mESCs were cultured on gelatin, supplemented by LIF+ mESC media to inhibit spontaneous differentiation of the cells.

extract_protocol:
Trizol was used to extract total RNA from the samples.
Sequencing libraries were constructed using the Illumina TruSeq Stranded mRNA kit. PolyA+ RNA was selected using poly-T oligo beads.

treatment_protocol: The cells were reverse-transfected with 20 uM of either eGFP, PTBP1 or PTBP1+PTBP2 siRNAs. After 24 hours, the attached cells were transfected again with the same amount of siRNAs for another 24 hours.

tag: fraction

value: CH

tag: molecule

value: polyA+ chromatin-associated RNA


title: 10007600-1


title: 10007567-1


title: siPTBP1+siPTBP2 CY Replicate 2

description: siPTBP1+siPTBP2 CY Replicate 2

value: CY

value: polyA+ cytoplasmic RNA


title: 10007566-1


title: 10007561-2


title: Human epicardial EV (Spindle) 2

description:
p222sS2_Cristina_S72_L008
Human spindle epic EV

value: extracellular vesicles (Evs)


title: 10007549-2


title: WT cells W/ RNase H-repeat 2

city: Saskatoon

first: Yuliang

last: Wu

state: Saskatchewan

address: Rm 4D01.1, HSB, 107 Wiggins Road

department: BMI

country: Canada

institute: University of Saskatchewan

description:
DNA:RNA hybrid
S00C5E0

library_source: genomic

data_processing:
ChIP/DRIP-Seq Adapter trimming: The adaptors of the paired-end FASTQ reads were trimmed using cutadapt (v1.18).
ChIP/DRIP-Seq Alignment: The trimmed reads were mapped to the hg38 human reference genome using Bowtie2 (v2.3.5).
ChIP/DRIP-Seq SAM to BAM / filtering: Mapped reads were converted from SAM format to BAM format and filtered based on mapping quality (>=10) using samtools view. Subsequent sorting was performed using samtools sort.
ChIP/DRIP-Seq BAM indexing: BAM files were indexed using samtools index.
ChIP/DRIP-Seq Peak calling: Peak-calling was performed using MACS2 (v2.2.1) and the following parameters: A genome size of 2.7e9, which is the recommended setting for the human genome; and a P-value cutoff of 1e-5. A negative control was supplied alongside the target data to correct for background.
ChIP/DRIP-Seq Motif detection: Motifs were extracted from the FASTA sequences of the peaks using MEME and the following options: fasta file uploaded as alphabet:custom;  "zoops" selected; number of motifs: 3; minimum width: 6; maximum width: 8
Genome_build: hg38
Supplementary_files_format_and_content: For the ChIP-Seq analysis, there are bedGraph files containing fragment pileup for both target and control. The bedGraph files were produced by MACS2 and used by MACS2 to determine statistically significant peaks.

molecule: genomic DNA

source_name: HT1080 cell nuclei

growth_protocol: HT1080 cells were grown in DMEM supplemented with 10% fetal bovine serum and penicillin/streptomycin (100 units/ml each).

extract_protocol:
The DNA was extracted with phenol-chloroform, precipitated with 2×volume of ethanol, washed with 70% ethanol, and dissolved in 50 µL of ddH2O. For RNA extraction and purification, Trizol reagent (Invitrogen) was used to isolate the sheared RNA. The isolated RNA was eluted in nuclease-free water.
The RNA library was prepared using the NEBNext Ultra II directional library prep kit (E7760, NEB) and DNA library by NEBNext ultra II DNA library prep kit (E7645, NEB) according to the manufacturer's instructions. Briefly, for RNA library preparation, the RNA extracted from the GRO reaction (described above, 1.5 µg) was converted into cDNA using random primers provided with the kit. The second strand was synthesized with NEBNext Second Strand Synthesis Reaction Buffer with dUTP and Enzyme Mix. The products were purified using 1.8× volume of AMPure beads and the cDNA eluted with nuclease-free water. This cDNA was end repaired, adaptor-ligated, cleaned up using 0.9× AMPure beads. The DNA was then amplified using 12 NEBNext Multiplex Oligos (Index primers 13-15, 18-23, 25 and 27) and universal primer (E7335, NEB) for the two independent experiments. The final products were cleaned using 0.9× AMPure beads.

treatment_protocol: WT and KO cells were used directly, no specific treatment was applied.

tag: passage

tag: antibody

value: S9.6 antibody (ENH001, Kerafast)


title: hNABP2 (hSSB1) KO cells-repeat 1

description:
DNA:RNA hybrid
S00C5DD

tag: cell line


title: 10007561-1


title: WT cells-repeat 2

description:
DNA:RNA hybrid
S00C5DF


title: hNABP2 (hSSB1) KO cells W/ RNase H1-repeat 2

description:
DNA:RNA hybrid
S00C5E5


title: 10007594-1


title: hNABP2 (hSSB1) KO cells-repeat 2

description:
DNA:RNA hybrid
S00C5E1


title: 10007544-1


title: WT cells W/O hNABP2 (hSSB1) ab pulldown-repeat 1

description:
DNA
S00A73E

value: Rabbit IgG


title: hNABP2 (hSSB1) KO cells W/ RNase H1-repeat 1

description:
DNA:RNA hybrid
S00C5DE


title: WT cells W/ RNase H-repeat 1

description:
DNA:RNA hybrid
S00C5DC


title: hNABP1 (hSSB2)-KO cells with NTP-repeat 3

description:
RNA
S00C5D8

value: BrdU antibody (SC-32323, Santa Cruz)


title: WT cells W/ hNABP2 (hSSB1) ab pulldown-repeat 2

description:
DNA
S00A743

value: hNABP2 (hSSB1) antibody (homemade)


title: WT cells-repeat 1

description:
DNA:RNA hybrid
S00C5DA


title: WT cells with NTP-repeat 3

description:
RNA
S00C5D4


title: 10007549-1


title: WT cells No NTP-repeat 3

description:
RNA
S00C5D1


title: WT cells W/ hNABP2 (hSSB1) ab pulldown-repeat 1

description:
DNA
S00A73F


title: hNABP2 (hSSB1)-KO cells with NTP-repeat 3

description:
RNA
S00C5D6


title: hNABP2 (hSSB1)-KO cells with NTP-repeat 2

description:
RNA
S00C5CF


title: hNABP1 (hSSB2)-KO cells No NTP-repeat 3

description:
RNA
S00C5D3


title: WT cells W/O hNABP2 (hSSB1) ab pulldown-repeat 2

description:
DNA
S00A742


title: hNABP2 (hSSB1)-KO cells No NTP-repeat 3

description:
RNA
S00C5D2


title: WT cells with NTP-repeat 2

description:
RNA
S00C5CD


title: hNABP2 (hSSB1)-KO cells No NTP-repeat 2

description:
RNA
S00C5CB


title: hNABP1 (hSSB2)-KO cells No NTP-repeat 2

description:
RNA
S00C5CC


title: WT cells with NTP-repeat 1

description:
RNA
S00A747


title: hNABP1 (hSSB2)-KO cells No NTP-repeat 1

description:
RNA
S00A746


title: hNABP1 (hSSB2)-KO cells with NTP-repeat 2

description:
RNA
S00C5D0


title: WT cells No NTP-repeat 1

description:
RNA
S00A744


title: hNABP2 (hSSB1)-KO cells with NTP-repeat 1

description:
RNA
S00A748


title: hNABP2 (hSSB1)-KO cells No NTP-repeat 1

description:
RNA
S00A745


title: hNABP1 (hSSB2)-KO cells with NTP-repeat 1

description:
RNA
S00A749


title: 48h reseed

city: St Louis

first: Samantha

last: Morris

state: Missouri

address: Department of Developmental Biology, Washington University School of

institute: Washington University in St Louis

description: Cells were encapsulted and library prepared using the 10X Chromium instrument with the Single Cell 3' Reagent Kits (v2 chemistry). BAM files and Gene-barcode matrices were generated using 10X Genomics Cellranger version 2(?)

data_processing:
Generation of fastq files via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Alignment to hg19 genome build via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Genome_build: hg19
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

molecule: polyA RNA

source_name: Embryonic stem cell

extract_protocol: 10x Genomcis Chromium single cell preparation

value: Embryonic stem cell


title: Gastruloid 44h sample 1


title: Gastruloid 44h sample 2


title: siPTBP1+siPTBP2 CH Replicate 2

description: siPTBP1+siPTBP2 CH Replicate 2

tag: treatment


title: siPTBP1 NP Replicate 3

description: siPTBP1 NP Replicate 3

value: NP

value: polyA+ nucleoplasm RNA


title: simBO -2

type: RNA

city: Daejeon

first: Jeongmin

last: Ha

address: 125, Gwahak-ro, Yuseong-gu

department: Stem Cell Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description: Gene expression of simBOs after differentiation day 10

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Human Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

source_name: pNSC-derived simBO, replicate 2

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: pNSCs were maintained in NSMM (50% Advanced DMEM/F12, 50% Neurobasal, 1x N2, 1x B27, 1% Glutmax, 0.5% Albumax, 10 ng/mL hLIF, 3 μM CHIR99021, and 2 μM SB431542) and differentiated with differentiation medium (DMEM/F12, 1x N2, 1x B27, 200 ng/mL dbcAMP, 5 μM DAPT, 10 ng/mL BDNF, and 10 ng/mL GDNF)

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: pNSC and 2D differentiation samples were cultured on geltrex-coated culture dish, and simBOs were cultured in bioreactor.

value: pNSC-derived simBO

tag: growth

value: 3D culture

tag: state

value: Differentiation


title: ACP02

city: Rio de Janeiro

first: Renata

last: Binato

state: Rio de Janeiro

address: Praça Cruz Vermelha 23/ 6 andar ala C

country: Brazil

institute: INCA

description: RMA expression value derived from Expression Console software; core-gene analysis

hyb_protocol: The biotinylated cRNA was subsequently hybridized to a GeneChip Human Exon 1.0 ST Array (Affymetrix, CA, USA).

scan_protocol: The GeneChip arrays were washed and stained according to the manufacturer’s protocols and scanned using a GeneChip® Scanner 3000 (Affymetrix)

data_processing: Affymetrix Expression Console Software version 1.0 was used to create summarized expression values (CHP-files). The Robust Multichip Analysis (RMA) algorithm was applied. The data were analyzed with Partek® software (http://www.partek.com).

label: biotin

source_name: primary diffuse adenocarcinoma

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: The cell lines were cultured in DMEM supplemented with 10% fetal bovine serum, 2 mM glutamine, 100 U/mL penicillin and 100 g/mL streptomycin. The flasks were maintained in a 5% CO2 incubator at 37°C.

extract_protocol: Total RNA from all cell lines used in this study was obtained using the RNeasy Mini Kit (Qiagen, CA, USA) according to the manufacturer's instructions.

value: cells stablished from a primary diffuse adenocarcinoma (T3N2M0)


title: AGP01

source_name: intestinal gastric adenocarcinoma

value: cells established from ascitic fluid cells from intestinal gastric adenocarcinoma (T3N2M1)


title: HK2 Empagliflozin 01

city: Innsbruck

first: Johannes

last: Leierer

address: Anichstr. 35

department: Internal Medicine IV - Nephrology

country: Austria

institute: Medical University Innsbruck

description: gene expression

hyb_protocol: Hybridization to oligonucleotide microarrays (Human GE 4x44K v2, G4845A) according to manufacturers protocol

scan_protocol: Arrays were scanned at 5 µm using an Axon Gene Pix 4000B scanner (Molecular Devices, Sunnyvale, CA) and signal intensity data extracted using Agilent Feature Extraction software (v.9.5.3.1).

data_processing: Data preprocessing consisted of (i) excluding low abundance features (intensity values < 1.5 above background signals), (ii) quantil-quantil data normalization, and (iii) summarization of identical sequence spots.

source_name: HK-2 mRNA

label_protocol: Cyanine 3 (Cy3) labelled cRNA was generated with the LowInput QuickAmp Labeling Kit (5190-2305) for hybridization to oligonucleotide microarrays (Human GE 4x44K v2, G4845A).

growth_protocol: Human kidney 2 (HK-2) cells obtained from American Type Culture Collection (Rockville, MD) were cultured in Keratinocyte–Serum-Free Medium (KSFM) containing 5,8 mmol/l glucose (i.e. normo-glycemic condition), 10% FBS, 5 ng/mL recombinant epidermal growth factor (rEGF), 0.05 mg/mL bovine pituitary extract (BPE), 100 units/mL penicillin, and 100 μg/mL streptomycin.  RPTEC/TERT1 cells obtained from Evercyte GmBH (Vienna, Austria) were propagated in DMEM-Ham's F-12 5 mmol/L glucose (1:1) medium supplemented with 5 μg/mL insulin, 5 μg/mL transferrin, 5 ng/mL sodium selenite, 10 ng/mL recombinant human EGF, 36 ng/mL hydrocortisone, 1X GlutaMAXTM, 100 units/mL penicillin and 100 μg/mL streptomycin. Cells were grown at 37°C in a humidified 5% CO2 atmosphere, and split at a 1:10 (HK2) or 1:6 (RPTEC/TERT1) ratio once a week or cultured to confluence, serum- and supplement-starved for 24 h, and then – after an additional medium change - used for experiments.

extract_protocol: After 24 hours total RNA was isolated with RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s protocol

treatment_protocol: Stimulations with empagliflocin (500nM) and IL‑1β (10ng/ml)

value: proximal tubule cellline


title: RPTEC control 01

description: gene expression


title: 2D differentiation 20d

description: Gene expression of 2D samples after differentiation day 20

source_name: 2D differentiation from pNSC, day 20

value: 2D differentiation from pNSC

value: 2D culture


title: simBO (3D) differentiation 10d

source_name: 3D differentiation from pNSC, day 10

value: 3D differentiation from pNSC


title: pNSC-1

description: Gene expression of pNSCs

source_name: Undifferentiated pNSC, replicate 1

value: Undifferentiated pNSC

value: Undifferentiation


title: pNSC-2

description: Gene expression of pNSCs

source_name: Undifferentiated pNSC, replicate 2


title: RPTEC Empagliflozin 02

description: gene expression


title: 2D differentiation 10d

description: Gene expression of 2D samples after differentiation day 10

source_name: 2D differentiation from pNSC, day 10


title: RPTEC control 02

description: gene expression


title: HK2 Interleukin1 02

description: gene expression


title: HK2 Interleukin1 01

description: gene expression


title: RPTEC Empagliflozin 01

description: gene expression


title: simBO (3D) differentiation 20d

description: Gene expression of simBOs after differentiation day 20

source_name: 3D differentiation from pNSC, day 20


title: simBO -1

source_name: pNSC-derived simBO, replicate 1


title: RPTEC Interleukin1 02

description: gene expression


title: HK2 control 02

description: gene expression


title: HK2  Empagliflozin 02

description: gene expression


title: HK2 control 01

description: gene expression


title: PCA.538: prostate_cancer_primary_538

city: Vancouver

first: Elai

last: Davicioni

state: BC

address: 1152 Mainland St, Suite 430

institute: Decipher Biosciences, Inc.

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

source_name: FFPE prostate cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by 2 expert genitourinary pathologists, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the prostatectomy FFPE block with the highest pathologic Gleason grade, regardless of its volume. Two 0.6-mm diameter tissue biopsy punch tool cores were sampled to enrich for tumor cells from the highest Gleason grade in the index lesion and placed in a microfuge tube for RNA extraction.

value: FFPE prostate cancer

tag: psa

tag: grade group

tag: non-organ confined

value: No

tag: plasma cell content

tag: inflammation signature

tag: ifng signature

tag: igg production

tag: nk activity


title: PCA.534: prostate_cancer_primary_534

tag: tissue

tag: age


title: PCA.532: prostate_cancer_primary_532


title: PCA.537: prostate_cancer_primary_537


title: PCA.536: prostate_cancer_primary_536

value: Yes


title: PCA.535: prostate_cancer_primary_535


title: PCA.530: prostate_cancer_primary_530


title: PCA.528: prostate_cancer_primary_528


title: RPTEC Interleukin1 01

description: gene expression


title: PCA.533: prostate_cancer_primary_533


title: PCA.529: prostate_cancer_primary_529


title: PCA.523: prostate_cancer_primary_523


title: PCA.525: prostate_cancer_primary_525


title: PCA.524: prostate_cancer_primary_524


title: PCA.516: prostate_cancer_primary_516


title: PCA.519: prostate_cancer_primary_519


title: PCA.531: prostate_cancer_primary_531


title: PCA.515: prostate_cancer_primary_515


title: PCA.520: prostate_cancer_primary_520


title: PCA.521: prostate_cancer_primary_521


title: PCA.517: prostate_cancer_primary_517


title: PCA.527: prostate_cancer_primary_527


title: PCA.513: prostate_cancer_primary_513


title: PCA.526: prostate_cancer_primary_526


title: PCA.511: prostate_cancer_primary_511


title: PCA.514: prostate_cancer_primary_514


title: PCA.522: prostate_cancer_primary_522


title: PCA.518: prostate_cancer_primary_518


title: PCA.512: prostate_cancer_primary_512


title: PCA.510: prostate_cancer_primary_510


title: PCA.507: prostate_cancer_primary_507


title: PCA.505: prostate_cancer_primary_505


title: PCA.506: prostate_cancer_primary_506


title: PCA.509: prostate_cancer_primary_509


title: PCA.504: prostate_cancer_primary_504


title: PCA.502: prostate_cancer_primary_502


title: PCA.501: prostate_cancer_primary_501


title: PCA.508: prostate_cancer_primary_508


title: WT cells No NTP-repeat 2

description:
RNA
S00C5CA

value: BrdU antibody (SC-32323, Santa Cruz)


title: PCA.499: prostate_cancer_primary_499


title: PCA.494: prostate_cancer_primary_494


title: PCA.500: prostate_cancer_primary_500


title: PCA.487: prostate_cancer_primary_487


title: PCA.497: prostate_cancer_primary_497


title: PCA.493: prostate_cancer_primary_493


title: PCA.496: prostate_cancer_primary_496


title: PCA.490: prostate_cancer_primary_490


title: PCA.489: prostate_cancer_primary_489


title: PCA.495: prostate_cancer_primary_495


title: PCA.491: prostate_cancer_primary_491


title: PCA.492: prostate_cancer_primary_492


title: PCA.478: prostate_cancer_primary_478


title: PCA.481: prostate_cancer_primary_481


title: PCA.488: prostate_cancer_primary_488


title: PCA.486: prostate_cancer_primary_486


title: PCA.476: prostate_cancer_primary_476


title: PCA.473: prostate_cancer_primary_473


title: PCA.484: prostate_cancer_primary_484


title: PCA.503: prostate_cancer_primary_503


title: PCA.485: prostate_cancer_primary_485


title: PCA.483: prostate_cancer_primary_483


title: PCA.482: prostate_cancer_primary_482


title: PCA.498: prostate_cancer_primary_498


title: PCA.471: prostate_cancer_primary_471


title: PCA.480: prostate_cancer_primary_480


title: PCA.475: prostate_cancer_primary_475


title: PCA.477: prostate_cancer_primary_477


title: PCA.474: prostate_cancer_primary_474


title: PCA.464: prostate_cancer_primary_464


title: PCA.479: prostate_cancer_primary_479


title: PCA.470: prostate_cancer_primary_470


title: PCA.459: prostate_cancer_primary_459


title: PCA.463: prostate_cancer_primary_463


title: PCA.453: prostate_cancer_primary_453


title: PCA.468: prostate_cancer_primary_468


title: PCA.465: prostate_cancer_primary_465


title: PCA.472: prostate_cancer_primary_472


title: PCA.469: prostate_cancer_primary_469


title: PCA.454: prostate_cancer_primary_454


title: PCA.467: prostate_cancer_primary_467


title: PCA.461: prostate_cancer_primary_461


title: PCA.448: prostate_cancer_primary_448


title: PCA.466: prostate_cancer_primary_466


title: PCA.450: prostate_cancer_primary_450


title: PCA.449: prostate_cancer_primary_449


title: PCA.457: prostate_cancer_primary_457


title: PCA.462: prostate_cancer_primary_462


title: PCA.458: prostate_cancer_primary_458


title: PCA.455: prostate_cancer_primary_455


title: PCA.456: prostate_cancer_primary_456


title: PCA.460: prostate_cancer_primary_460


title: PCA.452: prostate_cancer_primary_452


title: PCA.451: prostate_cancer_primary_451


title: PCA.443: prostate_cancer_primary_443


title: PCA.439: prostate_cancer_primary_439


title: PCA.445: prostate_cancer_primary_445


title: PCA.432: prostate_cancer_primary_432


title: PCA.434: prostate_cancer_primary_434


title: PCA.436: prostate_cancer_primary_436


title: PCA.444: prostate_cancer_primary_444


title: PCA.435: prostate_cancer_primary_435


title: PCA.438: prostate_cancer_primary_438


title: PCA.437: prostate_cancer_primary_437


title: PCA.440: prostate_cancer_primary_440


title: PCA.431: prostate_cancer_primary_431


title: PCA.446: prostate_cancer_primary_446


title: PCA.433: prostate_cancer_primary_433


title: PCA.429: prostate_cancer_primary_429


title: PCA.447: prostate_cancer_primary_447


title: PCA.442: prostate_cancer_primary_442


title: PCA.441: prostate_cancer_primary_441


title: PCA.423: prostate_cancer_primary_423


title: PCA.428: prostate_cancer_primary_428


title: PCA.424: prostate_cancer_primary_424


title: PCA.425: prostate_cancer_primary_425


title: PCA.430: prostate_cancer_primary_430


title: PCA.419: prostate_cancer_primary_419


title: PCA.418: prostate_cancer_primary_418


title: PCA.427: prostate_cancer_primary_427


title: PCA.421: prostate_cancer_primary_421


title: PCA.422: prostate_cancer_primary_422


title: PCA.412: prostate_cancer_primary_412


title: PCA.420: prostate_cancer_primary_420


title: PCA.417: prostate_cancer_primary_417


title: PCA.413: prostate_cancer_primary_413


title: PCA.415: prostate_cancer_primary_415


title: PCA.416: prostate_cancer_primary_416


title: PCA.411: prostate_cancer_primary_411


title: PCA.409: prostate_cancer_primary_409


title: PCA.410: prostate_cancer_primary_410


title: PCA.407: prostate_cancer_primary_407


title: PCA.405: prostate_cancer_primary_405


title: PCA.404: prostate_cancer_primary_404


title: PCA.399: prostate_cancer_primary_399


title: PCA.396: prostate_cancer_primary_396


title: PCA.414: prostate_cancer_primary_414


title: PCA.402: prostate_cancer_primary_402


title: PCA.400: prostate_cancer_primary_400


title: PCA.408: prostate_cancer_primary_408


title: PCA.391: prostate_cancer_primary_391


title: PCA.406: prostate_cancer_primary_406


title: PCA.403: prostate_cancer_primary_403


title: PCA.397: prostate_cancer_primary_397


title: PCA.393: prostate_cancer_primary_393


title: PCA.394: prostate_cancer_primary_394


title: PCA.395: prostate_cancer_primary_395


title: PCA.392: prostate_cancer_primary_392


title: PCA.390: prostate_cancer_primary_390


title: PCA.401: prostate_cancer_primary_401


title: PCA.398: prostate_cancer_primary_398


title: PCA.426: prostate_cancer_primary_426


title: PCA.389: prostate_cancer_primary_389


title: PCA.377: prostate_cancer_primary_377


title: PCA.380: prostate_cancer_primary_380


title: PCA.378: prostate_cancer_primary_378


title: PCA.384: prostate_cancer_primary_384


title: PCA.376: prostate_cancer_primary_376


title: PCA.388: prostate_cancer_primary_388


title: PCA.375: prostate_cancer_primary_375


title: PCA.381: prostate_cancer_primary_381


title: PCA.385: prostate_cancer_primary_385


title: PCA.386: prostate_cancer_primary_386


title: PCA.383: prostate_cancer_primary_383


title: PCA.371: prostate_cancer_primary_371


title: PCA.379: prostate_cancer_primary_379


title: PCA.360: prostate_cancer_primary_360


title: PCA.366: prostate_cancer_primary_366


title: PCA.387: prostate_cancer_primary_387


title: PCA.361: prostate_cancer_primary_361


title: PCA.362: prostate_cancer_primary_362


title: PCA.364: prostate_cancer_primary_364


title: PCA.369: prostate_cancer_primary_369


title: PCA.367: prostate_cancer_primary_367


title: PCA.370: prostate_cancer_primary_370


title: PCA.363: prostate_cancer_primary_363


title: PCA.372: prostate_cancer_primary_372


title: PCA.368: prostate_cancer_primary_368


title: PCA.382: prostate_cancer_primary_382


title: PCA.373: prostate_cancer_primary_373


title: PCA.374: prostate_cancer_primary_374


title: PCA.365: prostate_cancer_primary_365


title: PCA.359: prostate_cancer_primary_359


title: PCA.357: prostate_cancer_primary_357


title: PCA.355: prostate_cancer_primary_355


title: PCA.358: prostate_cancer_primary_358


title: PCA.353: prostate_cancer_primary_353


title: PCA.350: prostate_cancer_primary_350


title: PCA.356: prostate_cancer_primary_356


title: PCA.351: prostate_cancer_primary_351


title: PCA.352: prostate_cancer_primary_352


title: PCA.346: prostate_cancer_primary_346


title: PCA.349: prostate_cancer_primary_349


title: PCA.348: prostate_cancer_primary_348


title: PCA.344: prostate_cancer_primary_344


title: PCA.342: prostate_cancer_primary_342


title: PCA.343: prostate_cancer_primary_343


title: PCA.345: prostate_cancer_primary_345


title: PCA.347: prostate_cancer_primary_347


title: PCA.338: prostate_cancer_primary_338


title: PCA.335: prostate_cancer_primary_335


title: PCA.337: prostate_cancer_primary_337


title: PCA.340: prostate_cancer_primary_340


title: PCA.332: prostate_cancer_primary_332


title: PCA.334: prostate_cancer_primary_334


title: PCA.336: prostate_cancer_primary_336


title: PCA.331: prostate_cancer_primary_331


title: PCA.339: prostate_cancer_primary_339


title: PCA.341: prostate_cancer_primary_341


title: PCA.330: prostate_cancer_primary_330


title: PCA.333: prostate_cancer_primary_333


title: PCA.328: prostate_cancer_primary_328


title: PCA.329: prostate_cancer_primary_329


title: NC_PBMC

city: Shenzhen

first: Haiyan

last: YU

address: No. 1017, North of Dongmen Road

country: China

institute: Shenzhen People's Hospital

data_processing:
Barcode processing: To improve data quality, a ‘whitelist’ of correct barcode sequences was applied to fix the occasional sequencing error in barcodes obtained from the ‘I2’ index read
Genome alignment: Reference-based analysis was performed using the Cell Ranger ATAC pipeline. BWA-MEM was applied with default parameters to align the trimmed read pairs that were greater than 25 bp to GRCh38
Filteing: We filtered scATAC-seq data using cut-offs of 1,000 unique nuclear fragments per cell and a transcription start site (TSS) enrichment score of 8 to exclude low-quality cells in 10x genomic Cell Ranger ATAC platform
Peak calling: First, the number of transposition events at each base pair along the genome was counted. Next, a smoothed profile of these events with a 401 bp moving window around each base pair and fitting a ZINBA-like mixture model was generated. Then, a signal threshold was set to determine whether a region was a peak signal or noise based on an odds ratio of 1/5. Finally, peaks within 500 bp of each other were merged to produce a position-sorted BED file.
Cell calling and peak-barcode matrix: For each barcode, the mapped high-quality fragments that passed all filters were recorded, and the number of fragments that overlapped any peak regions was used to separate the signal from noise. To capture the signal and noise, a mixture model of two negative binomial distributions was set, and barcodes that corresponded to real cells from the non-cell barcodes were separated by setting an odds ratio of 1000. Subsequently, a raw peak-barcode matrix consisting of the counts of fragment ends within each peak region for each barcode was produced. After filtering to contain only cell barcodes, the matrix was used in subsequent analyses, such as dimensionality reduction, clustering and visualization.
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv files for barcodes; mtx files for matrix; bed files for peaks

source_name: Healthy controls

extract_protocol:
PBMCs were separated using an equal proportion of Ficoll-Paque Plus. Nuclei suspensions were obtained by adding lysis buffer (10 mM Tris-HCl, 3 mM MgCl2, 10 mM NaCl , 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 1% BSA). The final libraries were constructed via PCR with P5 and P7 primers in Illumina® bridge amplification.
scATAC-seq libraries were generated according to the Chromium Single Cell ATAC protocol (10x GENOMICS)

tag: disease state

value: Healthy controls

value: peripheral blood

tag: cell type

value: Peripheral blood mononuclear cells (PBMCs)


title: AS_PBMC

source_name: AS patients

value: AS patients


title: PCA.325: prostate_cancer_primary_325


title: PCA.322: prostate_cancer_primary_322


title: PCA.318: prostate_cancer_primary_318


title: PCA.319: prostate_cancer_primary_319


title: PCA.317: prostate_cancer_primary_317


title: PCA.324: prostate_cancer_primary_324


title: PCA.327: prostate_cancer_primary_327


title: PCA.314: prostate_cancer_primary_314


title: PCA.323: prostate_cancer_primary_323


title: PCA.316: prostate_cancer_primary_316


title: PCA.312: prostate_cancer_primary_312


title: PCA.308: prostate_cancer_primary_308


title: PCA.320: prostate_cancer_primary_320


title: PCA.326: prostate_cancer_primary_326


title: PCA.315: prostate_cancer_primary_315


title: PCA.321: prostate_cancer_primary_321


title: PCA.307: prostate_cancer_primary_307


title: PCA.310: prostate_cancer_primary_310


title: PCA.309: prostate_cancer_primary_309


title: PCA.306: prostate_cancer_primary_306


title: LCC2, biological rep3 [miRNA]

city: Suzhou

first: Min

last: Jiang

state: Jiangsu

address: No. 188, Shi Zi Road

institute: The First Affiliated Hospital of Soochow University

description:
TAM-4
Gene expression data from LCC2 cells.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix miRNA-4 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: LCC2 cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MCF-7, LCC2 and LCC9 cells were grown in phenol red free IMEM supplemented with 5% charcoal-stripped FBS and 1% penicillin/streptomycin in a cell culture incubator at 37 ℃ and 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: MCF-7, LCC2 or LCC9 cells were resuspended with phenol red free IMEM supplemented with 5% charcoal-stripped FBS and 1% penicillin/streptomycin and seeded in T75 flasks. Culture medium was changed once on day 2. Cells were washed with normal saline twice and harvested on day 4.

tag: tamoxifen resistance

value: tamoxifen-resistant

tag: fulvestrant resistance


title: LCC2, biological rep2 [miRNA]

description:
TAM-3
Gene expression data from LCC2 cells.

tag: cell line


title: PCA.313: prostate_cancer_primary_313


title: PCA.305: prostate_cancer_primary_305


title: PCA.311: prostate_cancer_primary_311


title: LCC2, biological rep1 [miRNA]

description:
TAM-2
Gene expression data from LCC2 cells.


title: PCA.304: prostate_cancer_primary_304


title: PCA.303: prostate_cancer_primary_303


title: MCF-7, biological rep1 [miRNA]

description:
S-1
Gene expression data from MCF-7 cells.

source_name: MCF-7 cell


title: MCF-7, biological rep3 [miRNA]

description:
S-6
Gene expression data from MCF-7 cells.


title: LCC9, biological rep3 [miRNA]

description:
FUL-5
Gene expression data from LCC9 cells.

source_name: LCC9 cell

value: fulvestrant-resistant


title: PCA.300: prostate_cancer_primary_300


title: LCC9, biological rep2 [miRNA]

description:
FUL-4
Gene expression data from LCC9 cells.


title: PCA.293: prostate_cancer_primary_293


title: PCA.299: prostate_cancer_primary_299


title: PCA.298: prostate_cancer_primary_298


title: PCA.294: prostate_cancer_primary_294


title: PCA.354: prostate_cancer_primary_354


title: PCA.295: prostate_cancer_primary_295


title: PCA.301: prostate_cancer_primary_301


title: PCA.297: prostate_cancer_primary_297


title: PCA.283: prostate_cancer_primary_283


title: PCA.284: prostate_cancer_primary_284


title: PCA.286: prostate_cancer_primary_286


title: PCA.287: prostate_cancer_primary_287


title: PCA.282: prostate_cancer_primary_282


title: PCA.289: prostate_cancer_primary_289


title: PCA.288: prostate_cancer_primary_288


title: PCA.292: prostate_cancer_primary_292


title: PCA.291: prostate_cancer_primary_291


title: PCA.296: prostate_cancer_primary_296


title: PCA.285: prostate_cancer_primary_285


title: LCC9, biological rep1 [miRNA]

description:
FUL-3
Gene expression data from LCC9 cells.


title: PCA.281: prostate_cancer_primary_281


title: PCA.280: prostate_cancer_primary_280


title: PCA.290: prostate_cancer_primary_290


title: PCA.279: prostate_cancer_primary_279


title: MCF-7, biological rep2 [miRNA]

description:
S-5
Gene expression data from MCF-7 cells.


title: PCA.277: prostate_cancer_primary_277


title: PCA.302: prostate_cancer_primary_302


title: PCA.275: prostate_cancer_primary_275


title: PCA.276: prostate_cancer_primary_276


title: PCA.270: prostate_cancer_primary_270


title: PCA.273: prostate_cancer_primary_273


title: PCA.269: prostate_cancer_primary_269


title: PCA.263: prostate_cancer_primary_263


title: PCA.262: prostate_cancer_primary_262


title: PCA.271: prostate_cancer_primary_271


title: PCA.265: prostate_cancer_primary_265


title: PCA.268: prostate_cancer_primary_268


title: PCA.264: prostate_cancer_primary_264


title: PCA.256: prostate_cancer_primary_256


title: PCA.266: prostate_cancer_primary_266


title: PCA.260: prostate_cancer_primary_260


title: PCA.274: prostate_cancer_primary_274


title: PCA.278: prostate_cancer_primary_278


title: PCA.272: prostate_cancer_primary_272


title: PCA.257: prostate_cancer_primary_257


title: PCA.259: prostate_cancer_primary_259


title: PCA.255: prostate_cancer_primary_255


title: PCA.254: prostate_cancer_primary_254


title: PCA.251: prostate_cancer_primary_251


title: PCA.261: prostate_cancer_primary_261


title: PCA.253: prostate_cancer_primary_253


title: PCA.267: prostate_cancer_primary_267


title: PCA.252: prostate_cancer_primary_252


title: PCA.250: prostate_cancer_primary_250


title: NKT_CD1d_b8

city: Beijing

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Raw reads were first trimmed by Cutadapt (v1.15) and clean reads for each individual cell were classified according to cell barcodes on Read#2. Then, Read#1 was aligned to the mm9 mouse transcriptome by Tophat (v2.0.12). After de-duplication based on UMIs, the transcript copy numbers of each gene were counted by HTseq (v0.10.0). Cells with more than 500 detected genes, and transcripts between 10,000 and 600,000 were retained. Then, cells with high ratio of ERCC spike-ins were further removed by the “isOutlier” function in the R package “scater”. The R package “Seurat” was adopted to perform the downstream analysis including identification of differentially expressed genes (DEGs, |ln(fold change)|>0.25 and adjust.p<0.05 were considered significant) and calculation of similarity scores.
Genome_build: mm9
Supplementary_files_format_and_content: NKT_countMatrix.txt: tab-delimited text file of count matrix. Cells have been filtered. barcode_annotations.xlsx: Excel file includes cell barcodes and annotations.

source_name: NKT Cells

extract_protocol:
Tissue preparation and cell isolation were performed as previously described. Briefly, the livers were perfused with PBS before extraction to remove the blood cell. Then, the livers were minced and filtered through a cell strainer (40 μm; BD Biosciences). Leukocytes were isolated from the liver cell suspensions by density fractionation using discontinuous 40-70% (vol/vol) Percoll (GE Healthcare) gradients, followed by red blood cell lysis before filtration. Then NKT cells were enriched by cell sorting (FACS) of NK1.1+CD3e+ cells and subjected to scRNA-seq.
First, individual cells were manually picked, lysed and subjected to first-strand cDNA synthesis as reported. Then, second-strand cDNA was synthesized, amplified and fragmented. RNA-seq libraries were prepared according to the instruction manual of the KAPA Hyper Prep Kit (KAPA Biosystems). Finally, the libraries were checked, pooled together and sequenced with paired-end 150-bp reads on an Illumina HiSeq X-Ten platform.

tag: strain

tag: genotype

value: Liver


title: PCA.258: prostate_cancer_primary_258

tag: psa


title: NKT_CD1d_b7


title: NKT_CD1d_b6


title: NKT_CD1d_b5


title: PCA.249: prostate_cancer_primary_249

tag: grade group


title: NKT_CD1d_b4


title: NKT_CD1d_b3


title: NKT_CD1d_b2


title: NKT_Ja18_b8


title: NKT_CD1d_b1


title: NKT_Ja18_b7


title: NKT_Ja18_b6


title: PCA.248: prostate_cancer_primary_248

tag: non-organ confined


title: NKT_Ja18_b5


title: NKT_Ja18_b4


title: NKT_Ja18_b3


title: PCA.247: prostate_cancer_primary_247

tag: plasma cell content


title: PCA.242: prostate_cancer_primary_242

tag: inflammation signature


title: PCA.243: prostate_cancer_primary_243

tag: ifng signature


title: PCA.244: prostate_cancer_primary_244

tag: igg production


title: NKT_Ja18_b2


title: PCA.245: prostate_cancer_primary_245

tag: nk activity


title: NKT_WT_b6

value: wild type

tag: tissue


title: NKT_WT_b7


title: NKT_WT_b8


title: NKT_Ja18_b1


title: PCA.241: prostate_cancer_primary_241

tag: age


title: PCA.246: prostate_cancer_primary_246


title: PCA.238: prostate_cancer_primary_238


title: PCA.234: prostate_cancer_primary_234


title: PCA.235: prostate_cancer_primary_235


title: NKT_WT_b5


title: PCA.240: prostate_cancer_primary_240


title: PCA.232: prostate_cancer_primary_232


title: PCA.239: prostate_cancer_primary_239


title: PCA.233: prostate_cancer_primary_233


title: PCA.237: prostate_cancer_primary_237


title: NKT_WT_b4


title: PCA.236: prostate_cancer_primary_236


title: NKT_WT_b2


title: PCA.231: prostate_cancer_primary_231


title: PCA.230: prostate_cancer_primary_230


title: NKT_WT_b1


title: Week3 FasDel rep 1

city: Denver

first: Satria

last: Sajuthi

state: Colorado

address: 1400 Jackson St.

institute: National Jewish Health

description:
norm_count.txt
raw_count.txt
RNA-seq
RE_9

data_processing:
Raw FASTQ files were trimmed with skewer
Trimmed reads were aligned to mouse transcriptome GRCm38 with HISAT2
Gene counting were performed with HTSEQ-count
Individual count table were combined with R statistical software to create a raw count matrix
Raw count matrix was then normalized by size factor with DESEQ2
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw gene count matrix and normalized gene count matrix in tab separated value file format

source_name: Primary lung fibroblast

extract_protocol:
Lineage negative cells were obtained by FACs sorting. At least 300,000 total cells were collected per population.   Purified cells were pelleted, lysed and RNA was precipitated using TRIzol (ThermoFisher Scientific) followed by purification of the aqueous layer using a RNeasy Micro Kit (Qiagen Sciences, Valencia, CA).
Bulk library: A modified Kapa Biosystems (Wilmington, MA, USA) KAPA Stranded mRNA-Seq kit for whole transcriptome libraries was used to primarily target all polyA RNA.   After mRNA (poly-A) isolation, 1st and 2nd strand cDNA synthesis, adaptor ligation, amplification, and bead templating occurred. Once validated, the libraries were sequenced as barcoded-pooled samples and processed for next-generation sequencing (NovaSeq 6000 - Illumina platform).    SC library: Cells were loaded onto a 10x Genomics  microfluidics chip and encapsulated with barcoded oligo-dT-containing gel beads using the 10x  Genomics Chromium controller and single-cell libraries constructed per the manufacturer’s  instructions. Samples were sequenced on a NovaSeq 6000 Illumina platform instrument (Illumina,   27  San Diego, CA).

tag: genotype/variation

value: Week3 FasDel

value: Fibroblast


title: SC week3 WT

description: 10X scRNA-seq

value: week3 WT


title: SC control

description: 10X scRNA-seq

value: control


title: SC week3 FasDel

description: 10X scRNA-seq

value: week3 FasDel


title: NKT_WT_b3


title: Week3 WT rep 3

description:
norm_count.txt
raw_count.txt
RNA-seq
RE_7

value: Week3 WT


title: Week3 WT rep 2

description:
norm_count.txt
raw_count.txt
RNA-seq
RE_6


title: Control rep 4

description:
norm_count.txt
raw_count.txt
RNA-seq
RE_4

value: Control


title: Week3 WT rep 1

description:
norm_count.txt
raw_count.txt
RNA-seq
RE_5


title: SC week6 FasDel

description: 10X scRNA-seq

value: week6 FasDel


title: PCA.228: prostate_cancer_primary_228

value: FFPE prostate cancer

value: No


title: Control rep 3

description:
norm_count.txt
raw_count.txt
RNA-seq
RE_3


title: PCA.225: prostate_cancer_primary_225

value: Yes


title: PCA.223: prostate_cancer_primary_223


title: PCA.219: prostate_cancer_primary_219


title: PCA.216: prostate_cancer_primary_216


title: PCA.217: prostate_cancer_primary_217


title: PCA.215: prostate_cancer_primary_215


title: PCA.221: prostate_cancer_primary_221


title: Week3 WT rep 4

description:
norm_count.txt
raw_count.txt
RNA-seq
RE_8


title: PCA.222: prostate_cancer_primary_222


title: PCA.226: prostate_cancer_primary_226


title: PCA.227: prostate_cancer_primary_227


title: PCA.218: prostate_cancer_primary_218


title: PCA.229: prostate_cancer_primary_229


title: PCA.214: prostate_cancer_primary_214


title: PCA.220: prostate_cancer_primary_220


title: PCA.224: prostate_cancer_primary_224


title: Week6 FasDel rep 4

description:
norm_count.txt
raw_count.txt
RNA-seq
RE_20

value: Week6 FasDel


title: Week6 FasDel rep 2

description:
norm_count.txt
raw_count.txt
RNA-seq
RE_18


title: Control rep 1

description:
norm_count.txt
raw_count.txt
RNA-seq
RE_1


title: Week6 FasDel rep 1

description:
norm_count.txt
raw_count.txt
RNA-seq
RE_17


title: PCA.212: prostate_cancer_primary_212


title: Week6 WT rep 4

description:
norm_count.txt
raw_count.txt
RNA-seq
RE_16

value: Week6 WT


title: Control rep 2

description:
norm_count.txt
raw_count.txt
RNA-seq
RE_2


title: PCA.211: prostate_cancer_primary_211


title: PCA.209: prostate_cancer_primary_209


title: Week6 WT rep 3

description:
norm_count.txt
raw_count.txt
RNA-seq
RE_15


title: Week6 WT rep 2

description:
norm_count.txt
raw_count.txt
RNA-seq
RE_14


title: PCA.210: prostate_cancer_primary_210


title: PCA.208: prostate_cancer_primary_208


title: Week3 FasDel rep 3

description:
norm_count.txt
raw_count.txt
RNA-seq
RE_11


title: Week3 FasDel rep 4

description:
norm_count.txt
raw_count.txt
RNA-seq
RE_12


title: Week6 FasDel rep 3

description:
norm_count.txt
raw_count.txt
RNA-seq
RE_19


title: Week6 WT rep 1

description:
norm_count.txt
raw_count.txt
RNA-seq
RE_13


title: PCA.207: prostate_cancer_primary_207


title: PCA.206: prostate_cancer_primary_206


title: Rbfox2 KD [M902]

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

data_processing:
Basecalls/demultiplexing performed using Illumina CASAVA 1.8.2
Aligned to mm10 using STAR2.4.0 (2 steps)
Count read using HT-seq0.6.1 using Ensembl GRCm38 as reference
Normalization (TMM), quantitation and differential expression analysis using EdgeR
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurement

source_name: Rbfox2 KD_whole retina

growth_protocol: Six month old mice were used

extract_protocol:
Total retinal RNA was isolated with an RNeasy mini kit (Qiagen, Germantown, MD)
Nugen Universal Plus mRNA-seq library preparation kit (Tecan Genomics, Redwood City, CA)

treatment_protocol: Rbfox2 downregulation was induced by tamoxifen treatment for 4 months

tag: strain background

value: Rbfox2 KD

value: 6 months

value: whole retina


title: Rbfox2 KD [M909]


title: SC week6 WT

description: 10X scRNA-seq

value: week6 WT


title: PCA.203: prostate_cancer_primary_203


title: Rbfox2 KD [M901]


title: Rbfox2 KD [M893]


title: PCA.201: prostate_cancer_primary_201


title: PCA.205: prostate_cancer_primary_205


title: PCA.200: prostate_cancer_primary_200


title: PCA.213: prostate_cancer_primary_213


title: control [M896]

source_name: control_whole retina


title: control [M894]


title: control [M898]


title: Week3 FasDel rep 2

description:
norm_count.txt
raw_count.txt
RNA-seq
RE_10

value: Week3 FasDel


title: control [M833]


title: PCA.198: prostate_cancer_primary_198


title: PCA.202: prostate_cancer_primary_202


title: PCA.199: prostate_cancer_primary_199


title: ATACseq of MA1L_sgKmt2d, 0_IFNG replicate 2

city: West Haven

first: Ryan

middle: D

last: Chow

state: CT

address: 850 West Campus Drive

institute: Yale University

data_processing:
Reads were aligned to the mm10 genome with Bowtie v2.2.9
ATAC-seq accessible regions were called with MACS2.
Reads spanning ATAC-seq regions were quantified and tabulated across all samples using DiffBind.
Differential accessibility was determined using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: peak calls for each sample
Supplementary_files_format_and_content: Read counts for all ATAC-seq regions across all samples

source_name: MA1L liver cancer cells

extract_protocol:
200,000 of vector or sgKmt2d transduced primary liver tumor cells (MA1L) were seeded into 12-well plate, and 0, or 10 ng/ml IFN-γ were added to treated them for 24 h. After treatment, the cell nuclei were collected for ATAC-seq using a protocol as previously described. Briefly, cells from different treatment group were counted and 50,000 cells were collected by centrifuge at 500g for 5 min. After washing once with 50 μl of cold 1× PBS, the cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630).
Immediately after lysis, nuclei were spun at 500 g for 10 min using a refrigerated centrifuge, and the pellet was resuspended in the transposase reaction mix (25 μl 2× TD buffer, 2.5 μl transposase (Illumina) and 22.5 μl nuclease-free water). The transposition reaction was carried out for 30 min at 37°C. After transposition reaction, the sample was purified using a Qiagen MinElute kit, and using 1× NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2 using the following PCR conditions: 72°C for 5 min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. To assure the PCR cycles, the full libraries were amplified for five cycles, and then 5 μl was used for Sybr Green qPCR. After determing the cycle number, the remaining 45 μl were amplified. The libraries were purified using AMPure XP beads.

tag: transduction

tag: treatment

value: DMSO

tag: genetic  background

value: p53-/-, Myc overexpression; C57BL/6J


title: PCA.195: prostate_cancer_primary_195


title: PCA.196: prostate_cancer_primary_196


title: PCA.197: prostate_cancer_primary_197


title: ATACseq of MA1L_sgKmt2d, 10_IFNG replicate 1

value: 10 ng/ml IFNG


title: ATACseq of MA1L_sgKmt2d, 10_IFNG replicate 3


title: ATACseq of MA1L_sgKmt2d, 0_IFNG replicate 3


title: ATACseq of MA1L_sgKmt2d, 10_IFNG replicate 2


title: PCA.204: prostate_cancer_primary_204


title: PCA.193: prostate_cancer_primary_193


title: PCA.194: prostate_cancer_primary_194


title: ATACseq of MA1L_sgKmt2d, 0_IFNG replicate 1


title: PCA.192: prostate_cancer_primary_192


title: ATACseq of MA1L_vector, 10_IFNG replicate 2

value: Vector


title: ATACseq of MA1L_vector, 10_IFNG replicate 3


title: PCA.190: prostate_cancer_primary_190


title: ATACseq of MA1L_vector, 0_IFNG replicate 3


title: PCA.189: prostate_cancer_primary_189


title: PCA.188: prostate_cancer_primary_188


title: ATACseq of MA1L_vector, 10_IFNG replicate 1


title: PCA.187: prostate_cancer_primary_187


title: PCA.186: prostate_cancer_primary_186


title: ATACseq of MA1L_vector, 0_IFNG replicate 2


title: ATACseq of MA1L_vector, 0_IFNG replicate 1


title: PCA.183: prostate_cancer_primary_183


title: PCA.185: prostate_cancer_primary_185


title: PCA.181: prostate_cancer_primary_181


title: PCA.184: prostate_cancer_primary_184


title: PCA.191: prostate_cancer_primary_191


title: PCA.174: prostate_cancer_primary_174


title: PCA.179: prostate_cancer_primary_179


title: PCA.180: prostate_cancer_primary_180


title: PCA.178: prostate_cancer_primary_178


title: PCA.173: prostate_cancer_primary_173


title: PCA.176: prostate_cancer_primary_176


title: PCA.177: prostate_cancer_primary_177


title: PCA.175: prostate_cancer_primary_175


title: PCA.182: prostate_cancer_primary_182


title: PCA.172: prostate_cancer_primary_172


title: PCA.170: prostate_cancer_primary_170


title: PCA.169: prostate_cancer_primary_169


title: PCA.168: prostate_cancer_primary_168


title: PCA.171: prostate_cancer_primary_171


title: PCA.166: prostate_cancer_primary_166


title: Genomic DNA from blood 300

type: genomic

city: Exeter

first: Katie

last: Lunnon

state: Devon

address: RILD South, Barrack Road

country: United Kingdom

institute: University of Exeter

description: Alzheimer's disease sample

hyb_protocol: DNA was sodium-bisulfite treated using a Zymo EZ-96 DNA methylation kit, and was subsequently amplified, fragmented and hybridised to Illumina Infinium HumanMethylation 450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner settings

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from whole blood samples using Qiagen DNeasy Kit according to standard instructions

value: whole blood

tag: Sex

value: Female

tag: disease state

value: Alzheimer's disease

tag: disease state2

value: Included


title: PCA.167: prostate_cancer_primary_167

value: FFPE prostate cancer

tag: psa

tag: grade group

value: No


title: PCA.163: prostate_cancer_primary_163

tag: non-organ confined

tag: plasma cell content


title: Genomic DNA from blood 298

description: Alzheimer's disease sample


title: Genomic DNA from blood 299

description: Alzheimer's disease sample

value: Male


title: PCA.162: prostate_cancer_primary_162

tag: inflammation signature

tag: ifng signature


title: PCA.164: prostate_cancer_primary_164

value: Yes

tag: igg production

tag: nk activity


title: PCA.165: prostate_cancer_primary_165

tag: tissue

tag: age


title: Genomic DNA from blood 295

description: mild cognitive impairment sample

value: mild cognitive impairment

value: mild cognitive impairment stable


title: PCA.159: prostate_cancer_primary_159


title: PCA.160: prostate_cancer_primary_160


title: Genomic DNA from blood 296

description: mild cognitive impairment sample


title: Genomic DNA from blood 293

description: Alzheimer's disease sample


title: Genomic DNA from blood 291

description: Alzheimer's disease sample


title: Genomic DNA from blood 297

description: control sample

value: control


title: Genomic DNA from blood 294

description: mild cognitive impairment sample

value: mild cognitive impairment to alzheimer's disease converter


title: Genomic DNA from blood 289

description: Alzheimer's disease sample

value: Excluded


title: Genomic DNA from blood 292

description: mild cognitive impairment sample


title: PCA.157: prostate_cancer_primary_157


title: Genomic DNA from blood 288

description: control sample


title: PCA.158: prostate_cancer_primary_158


title: Genomic DNA from blood 283

description: mild cognitive impairment sample


title: PCA.156: prostate_cancer_primary_156


title: Genomic DNA from blood 290

description: control sample


title: Genomic DNA from blood 287

description: mild cognitive impairment sample


title: Genomic DNA from blood 286

description: Alzheimer's disease sample


title: Genomic DNA from blood 285

description: control sample


title: PCA.152: prostate_cancer_primary_152


title: PCA.154: prostate_cancer_primary_154


title: PCA.161: prostate_cancer_primary_161


title: Genomic DNA from blood 284

description: mild cognitive impairment sample


title: PCA.151: prostate_cancer_primary_151


title: Genomic DNA from blood 282

description: mild cognitive impairment sample


title: PCA.150: prostate_cancer_primary_150


title: Genomic DNA from blood 279

description: mild cognitive impairment sample


title: PCA.147: prostate_cancer_primary_147


title: PCA.148: prostate_cancer_primary_148


title: Genomic DNA from blood 280

description: Alzheimer's disease sample


title: PCA.149: prostate_cancer_primary_149


title: PCA.146: prostate_cancer_primary_146


title: Genomic DNA from blood 274

description: Alzheimer's disease sample


title: Genomic DNA from blood 277

description: Alzheimer's disease sample


title: PCA.153: prostate_cancer_primary_153


title: Genomic DNA from blood 275

description: Alzheimer's disease sample


title: Genomic DNA from blood 281

description: control sample


title: PCA.143: prostate_cancer_primary_143


title: PCA.145: prostate_cancer_primary_145


title: PCA.144: prostate_cancer_primary_144


title: PCA.140: prostate_cancer_primary_140


title: Genomic DNA from blood 276

description: Alzheimer's disease sample


title: Genomic DNA from blood 271

description: control sample


title: Genomic DNA from blood 272

description: Alzheimer's disease sample


title: PCA.142: prostate_cancer_primary_142


title: Genomic DNA from blood 268

description: control sample


title: Genomic DNA from blood 266

description: mild cognitive impairment sample


title: Genomic DNA from blood 278

description: mild cognitive impairment sample


title: PCA.155: prostate_cancer_primary_155


title: PCA.141: prostate_cancer_primary_141


title: PCA.139: prostate_cancer_primary_139


title: Genomic DNA from blood 267

description: mild cognitive impairment sample


title: PCA.138: prostate_cancer_primary_138


title: Genomic DNA from blood 270

description: mild cognitive impairment sample


title: Genomic DNA from blood 273

description: control sample


title: Genomic DNA from blood 262

description: mild cognitive impairment sample


title: Genomic DNA from blood 265

description: control sample


title: PCA.136: prostate_cancer_primary_136


title: PCA.137: prostate_cancer_primary_137


title: PCA.134: prostate_cancer_primary_134


title: Genomic DNA from blood 263

description: Alzheimer's disease sample


title: Genomic DNA from blood 261

description: mild cognitive impairment sample


title: PCA.130: prostate_cancer_primary_130


title: PCA.135: prostate_cancer_primary_135


title: PCA.133: prostate_cancer_primary_133


title: PCA.132: prostate_cancer_primary_132


title: Genomic DNA from blood 264

description: control sample


title: PCA.131: prostate_cancer_primary_131


title: Genomic DNA from blood 260

description: mild cognitive impairment sample


title: PCA.128: prostate_cancer_primary_128


title: PCA.126: prostate_cancer_primary_126


title: Genomic DNA from blood 256

description: Alzheimer's disease sample


title: PCA.129: prostate_cancer_primary_129


title: PCA.125: prostate_cancer_primary_125


title: PCA.127: prostate_cancer_primary_127


title: PCA.124: prostate_cancer_primary_124


title: PCA.121: prostate_cancer_primary_121


title: Genomic DNA from blood 249

description: mild cognitive impairment sample


title: PCA.120: prostate_cancer_primary_120


title: Genomic DNA from blood 254

description: mild cognitive impairment sample


title: PCA.122: prostate_cancer_primary_122


title: PCA.123: prostate_cancer_primary_123


title: Genomic DNA from blood 251

description: mild cognitive impairment sample


title: Genomic DNA from blood 257

description: mild cognitive impairment sample


title: Genomic DNA from blood 252

description: control sample


title: Genomic DNA from blood 255

description: control sample


title: Genomic DNA from blood 250

description: mild cognitive impairment sample


title: Genomic DNA from blood 269

description: mild cognitive impairment sample


title: Genomic DNA from blood 258

description: Alzheimer's disease sample


title: PCA.118: prostate_cancer_primary_118


title: Genomic DNA from blood 253

description: mild cognitive impairment sample


title: PCA.119: prostate_cancer_primary_119


title: PCA.117: prostate_cancer_primary_117


title: Genomic DNA from blood 248

description: mild cognitive impairment sample


title: Genomic DNA from blood 247

description: mild cognitive impairment sample


title: Genomic DNA from blood 245

description: control sample


title: PCA.114: prostate_cancer_primary_114


title: Genomic DNA from blood 241

description: control sample


title: PCA.116: prostate_cancer_primary_116


title: PCA.115: prostate_cancer_primary_115


title: PCA.111: prostate_cancer_primary_111


title: Genomic DNA from blood 240

description: Alzheimer's disease sample


title: Genomic DNA from blood 246

description: mild cognitive impairment sample


title: Genomic DNA from blood 243

description: control sample


title: PCA.113: prostate_cancer_primary_113


title: Genomic DNA from blood 242

description: Alzheimer's disease sample


title: PCA.112: prostate_cancer_primary_112


title: PCA.108: prostate_cancer_primary_108


title: PCA.109: prostate_cancer_primary_109


title: Genomic DNA from blood 244

description: control sample


title: Genomic DNA from blood 238

description: mild cognitive impairment sample


title: PCA.110: prostate_cancer_primary_110


title: Genomic DNA from blood 239

description: control sample


title: PCA.107: prostate_cancer_primary_107


title: PCA.105: prostate_cancer_primary_105


title: PCA.106: prostate_cancer_primary_106


title: PCA.102: prostate_cancer_primary_102


title: Genomic DNA from blood 236

description: Alzheimer's disease sample


title: Genomic DNA from blood 229

description: Alzheimer's disease sample


title: PCA.103: prostate_cancer_primary_103


title: PCA.101: prostate_cancer_primary_101


title: PCA.100: prostate_cancer_primary_100


title: Genomic DNA from blood 233

description: Alzheimer's disease sample


title: Genomic DNA from blood 237

description: mild cognitive impairment sample


title: PCA.99: prostate_cancer_primary_99


title: Genomic DNA from blood 231

description: Alzheimer's disease sample


title: Genomic DNA from blood 234

description: mild cognitive impairment sample


title: Genomic DNA from blood 228

description: Alzheimer's disease sample


title: Genomic DNA from blood 235

description: control sample


title: Genomic DNA from blood 232

description: Alzheimer's disease sample


title: PCA.104: prostate_cancer_primary_104


title: Genomic DNA from blood 259

description: mild cognitive impairment sample


title: PCA.98: prostate_cancer_primary_98


title: Genomic DNA from blood 227

description: control sample


title: Genomic DNA from blood 230

description: control sample


title: Genomic DNA from blood 222

description: mild cognitive impairment sample


title: Genomic DNA from blood 224

description: mild cognitive impairment sample


title: PCA.95: prostate_cancer_primary_95


title: PCA.96: prostate_cancer_primary_96


title: Genomic DNA from blood 226

description: Alzheimer's disease sample


title: Genomic DNA from blood 223

description: Alzheimer's disease sample


title: Genomic DNA from blood 225

description: Alzheimer's disease sample


title: Genomic DNA from blood 220

description: mild cognitive impairment sample


title: PCA.97: prostate_cancer_primary_97


title: PCA.94: prostate_cancer_primary_94


title: PCA.90: prostate_cancer_primary_90


title: PCA.92: prostate_cancer_primary_92


title: Genomic DNA from blood 218

description: mild cognitive impairment sample


title: PCA.88: prostate_cancer_primary_88


title: PCA.89: prostate_cancer_primary_89


title: PCA.91: prostate_cancer_primary_91


title: Genomic DNA from blood 217

description: mild cognitive impairment sample


title: PCA.93: prostate_cancer_primary_93


title: Genomic DNA from blood 214

description: mild cognitive impairment sample


title: PCA.87: prostate_cancer_primary_87


title: PCA.86: prostate_cancer_primary_86


title: PCA.85: prostate_cancer_primary_85


title: PCA.84: prostate_cancer_primary_84


title: PCA.83: prostate_cancer_primary_83


title: Genomic DNA from blood 215

description: mild cognitive impairment sample

value: unknown


title: PCA.81: prostate_cancer_primary_81


title: Genomic DNA from blood 216

description: mild cognitive impairment sample


title: PCA.78: prostate_cancer_primary_78


title: PCA.79: prostate_cancer_primary_79


title: Genomic DNA from blood 213

description: Alzheimer's disease sample


title: Genomic DNA from blood 211

description: control sample


title: Genomic DNA from blood 208

description: mild cognitive impairment sample


title: Genomic DNA from blood 210

description: Alzheimer's disease sample


title: PCA.76: prostate_cancer_primary_76


title: PCA.77: prostate_cancer_primary_77


title: PCA.75: prostate_cancer_primary_75


title: PCA.80: prostate_cancer_primary_80


title: Genomic DNA from blood 207

description: mild cognitive impairment sample


title: Genomic DNA from blood 219

description: control sample


title: Genomic DNA from blood 221

description: mild cognitive impairment sample


title: Genomic DNA from blood 204

description: control sample


title: Genomic DNA from blood 203

description: control sample


title: Genomic DNA from blood 205

description: Alzheimer's disease sample


title: Genomic DNA from blood 209

description: Alzheimer's disease sample


title: Genomic DNA from blood 212

description: mild cognitive impairment sample


title: PCA.73: prostate_cancer_primary_73


title: Genomic DNA from blood 206

description: control sample


title: PCA.71: prostate_cancer_primary_71


title: Genomic DNA from blood 201

description: control sample


title: PCA.72: prostate_cancer_primary_72


title: PCA.70: prostate_cancer_primary_70


title: PCA.69: prostate_cancer_primary_69


title: Genomic DNA from blood 196

description: mild cognitive impairment sample


title: PCA.82: prostate_cancer_primary_82


title: Genomic DNA from blood 195

description: mild cognitive impairment sample


title: Genomic DNA from blood 202

description: control sample


title: PCA.67: prostate_cancer_primary_67


title: PCA.66: prostate_cancer_primary_66


title: PCA.65: prostate_cancer_primary_65


title: Genomic DNA from blood 197

description: control sample


title: PCA.64: prostate_cancer_primary_64


title: Genomic DNA from blood 198

description: control sample


title: Genomic DNA from blood 194

description: Alzheimer's disease sample


title: PCA.63: prostate_cancer_primary_63


title: PCA.62: prostate_cancer_primary_62


title: Genomic DNA from blood 188

description: mild cognitive impairment sample


title: Genomic DNA from blood 199

description: mild cognitive impairment sample


title: PCA.61: prostate_cancer_primary_61


title: PCA.59: prostate_cancer_primary_59


title: PCA.60: prostate_cancer_primary_60


title: Genomic DNA from blood 185

description: control sample


title: Genomic DNA from blood 187

description: mild cognitive impairment sample


title: Genomic DNA from blood 189

description: Alzheimer's disease sample


title: PCA.74: prostate_cancer_primary_74


title: Genomic DNA from blood 191

description: control sample


title: Genomic DNA from blood 192

description: control sample


title: PCA.68: prostate_cancer_primary_68


title: Genomic DNA from blood 193

description: mild cognitive impairment sample


title: Genomic DNA from blood 186

description: Alzheimer's disease sample


title: PCA.58: prostate_cancer_primary_58


title: Genomic DNA from blood 190

description: control sample


title: PCA.54: prostate_cancer_primary_54


title: PCA.57: prostate_cancer_primary_57


title: PCA.56: prostate_cancer_primary_56


title: Genomic DNA from blood 183

description: mild cognitive impairment sample


title: Genomic DNA from blood 180

description: mild cognitive impairment sample


title: Genomic DNA from blood 177

description: control sample


title: PCA.53: prostate_cancer_primary_53


title: PCA.50: prostate_cancer_primary_50


title: PCA.52: prostate_cancer_primary_52


title: PCA.51: prostate_cancer_primary_51


title: PCA.55: prostate_cancer_primary_55


title: PCA.49: prostate_cancer_primary_49


title: PCA.48: prostate_cancer_primary_48


title: Genomic DNA from blood 200

description: mild cognitive impairment sample


title: Genomic DNA from blood 181

description: control sample


title: Genomic DNA from blood 179

description: mild cognitive impairment sample


title: PCA.44: prostate_cancer_primary_44


title: PCA.45: prostate_cancer_primary_45


title: PCA.46: prostate_cancer_primary_46


title: PCA.47: prostate_cancer_primary_47


title: Genomic DNA from blood 176

description: Alzheimer's disease sample


title: PCA.43: prostate_cancer_primary_43


title: Genomic DNA from blood 174

description: mild cognitive impairment sample


title: Genomic DNA from blood 184

description: Alzheimer's disease sample


title: PCA.41: prostate_cancer_primary_41


title: Genomic DNA from blood 167

description: control sample


title: PCA.40: prostate_cancer_primary_40


title: Genomic DNA from blood 182

description: control sample


title: Genomic DNA from blood 173

description: mild cognitive impairment sample


title: PCA.42: prostate_cancer_primary_42


title: Genomic DNA from blood 169

description: Alzheimer's disease sample


title: Genomic DNA from blood 175

description: Alzheimer's disease sample


title: Genomic DNA from blood 168

description: control sample


title: Genomic DNA from blood 178

description: control sample


title: PCA.38: prostate_cancer_primary_38


title: PCA.39: prostate_cancer_primary_39


title: Genomic DNA from blood 171

description: Alzheimer's disease sample


title: Genomic DNA from blood 166

description: mild cognitive impairment sample


title: Genomic DNA from blood 172

description: Alzheimer's disease sample


title: Genomic DNA from blood 170

description: mild cognitive impairment sample


title: Genomic DNA from blood 165

description: control sample


title: PCA.35: prostate_cancer_primary_35


title: PCA.36: prostate_cancer_primary_36


title: PCA.32: prostate_cancer_primary_32


title: PCA.37: prostate_cancer_primary_37


title: PCA.31: prostate_cancer_primary_31


title: Genomic DNA from blood 161

description: mild cognitive impairment sample


title: Genomic DNA from blood 163

description: mild cognitive impairment sample


title: Genomic DNA from blood 162

description: control sample


title: Genomic DNA from blood 164

description: control sample


title: PCA.29: prostate_cancer_primary_29


title: PCA.34: prostate_cancer_primary_34


title: PCA.30: prostate_cancer_primary_30


title: Genomic DNA from blood 160

description: mild cognitive impairment sample


title: Genomic DNA from blood 156

description: Alzheimer's disease sample


title: Genomic DNA from blood 158

description: control sample


title: Genomic DNA from blood 157

description: control sample


title: PCA.24: prostate_cancer_primary_24


title: PCA.25: prostate_cancer_primary_25


title: Genomic DNA from blood 159

description: mild cognitive impairment sample


title: PCA.28: prostate_cancer_primary_28


title: PCA.26: prostate_cancer_primary_26


title: Genomic DNA from blood 151

description: mild cognitive impairment sample


title: Genomic DNA from blood 152

description: Alzheimer's disease sample


title: PCA.27: prostate_cancer_primary_27


title: Genomic DNA from blood 153

description: control sample


title: PCA.23: prostate_cancer_primary_23


title: Genomic DNA from blood 155

description: Alzheimer's disease sample


title: PCA.33: prostate_cancer_primary_33


title: PCA.20: prostate_cancer_primary_20


title: PCA.22: prostate_cancer_primary_22


title: PCA.17: prostate_cancer_primary_17


title: PCA.18: prostate_cancer_primary_18


title: Genomic DNA from blood 147

description: Alzheimer's disease sample


title: Genomic DNA from blood 149

description: Alzheimer's disease sample


title: Genomic DNA from blood 144

description: Alzheimer's disease sample


title: PCA.21: prostate_cancer_primary_21


title: Genomic DNA from blood 143

description: Alzheimer's disease sample


title: Genomic DNA from blood 146

description: mild cognitive impairment sample


title: PCA.16: prostate_cancer_primary_16


title: Genomic DNA from blood 150

description: mild cognitive impairment sample


title: Genomic DNA from blood 145

description: control sample


title: Genomic DNA from blood 148

description: control sample


title: PCA.14: prostate_cancer_primary_14


title: PCA.13: prostate_cancer_primary_13


title: PCA.12: prostate_cancer_primary_12


title: Genomic DNA from blood 139

description: mild cognitive impairment sample


title: PCA.11: prostate_cancer_primary_11


title: PCA.8: prostate_cancer_primary_8


title: PCA.6: prostate_cancer_primary_6


title: Genomic DNA from blood 142

description: Alzheimer's disease sample


title: PCA.9: prostate_cancer_primary_9


title: PCA.10: prostate_cancer_primary_10


title: PCA.7: prostate_cancer_primary_7


title: Genomic DNA from blood 137

description: control sample


title: Genomic DNA from blood 154

description: Alzheimer's disease sample


title: Genomic DNA from blood 133

description: mild cognitive impairment sample


title: Genomic DNA from blood 135

description: control sample


title: Genomic DNA from blood 138

description: control sample


title: PCA.5: prostate_cancer_primary_5


title: Genomic DNA from blood 140

description: control sample


title: PCA.4: prostate_cancer_primary_4


title: PCA.19: prostate_cancer_primary_19


title: PCA.15: prostate_cancer_primary_15


title: Genomic DNA from blood 141

description: mild cognitive impairment sample


title: PCA.3: prostate_cancer_primary_3


title: PCA.300: prostate_cancer_primary_300

tag: race

value: White

tag: palsma cell content


title: Genomic DNA from blood 132

description: control sample


title: PCA.1: prostate_cancer_primary_1


title: Genomic DNA from blood 136

description: mild cognitive impairment sample


title: Genomic DNA from blood 134

description: control sample


title: Genomic DNA from blood 131

description: mild cognitive impairment sample


title: CS2370_iec5_rep2_RNA

city: New York

first: Songtao

last: Jia

state: New York

address: 116th & Broadway

department: Biological Sciences

institute: Columbia University

description: rRNA-depleted RNA

data_processing:
RNA-seq reads of each sample were mapped to the genome assembly of Schizosaccharomyces pombe using HISAT2 (v2.1.0). The mapped reads count of each gene was measured by featureCounts (v1.6.1). The differential gene expression was calculated and visualized by the R packages DESeq2 (v1.28.0) and ggplot2 (v3.2.1).
Genome_build: ASM294v2
Supplementary_files_format_and_content: The mapped reads count of each gene was measured by featureCounts (v1.6.1) and presented as a table.

organism: Schizosaccharomyces pombe

growth_protocol: Cells were grown in YEA until mid-log phase

extract_protocol:
Total cellular RNA was isolated from log-phase cells using MasterPure yeast RNA purification kit (Epicentre) according to the manufacturer’s protocol. the total RNA was treated with RiboMinus™ Transcriptome Isolation Kit (ThermoFisher Scientific, K155003) to deplete rRNA.
The rRNA-depleted samples were used to construct strand-specific sequencing libraries with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB, E7760).

tag: genotype

tag: media

value: YEA


title: PCA.2: prostate_cancer_primary_2


title: CS2379_iec1_rep2_RNA

description: rRNA-depleted RNA


title: Genomic DNA from blood 125

description: control sample

tag: Sex


title: Genomic DNA from blood 130

description: control sample

tag: disease state


title: Genomic DNA from blood 126

description: mild cognitive impairment sample

tag: disease state2


title: CS2354_nht1_rep2_RNA

description: rRNA-depleted RNA


title: PCA.299: prostate_cancer_primary_299

tag: psa


title: Genomic DNA from blood 127

description: mild cognitive impairment sample


title: Genomic DNA from blood 128

description: Alzheimer's disease sample


title: SPJ1577_wt_rep2_RNA

description: rRNA-depleted RNA

value: WT


title: Genomic DNA from blood 124

description: mild cognitive impairment sample

value: whole blood


title: Genomic DNA from blood 122

description: Alzheimer's disease sample

value: Female


title: Genomic DNA from blood 123

description: mild cognitive impairment sample


title: CS2370_iec5_rep1_RNA

description: rRNA-depleted RNA


title: Genomic DNA from blood 129

description: control sample


title: PCA.298: prostate_cancer_primary_298

tag: grade group


title: CS2379_iec1_rep1_RNA

description: rRNA-depleted RNA


title: PCA.297: prostate_cancer_primary_297

tag: non-organ confined


title: Genomic DNA from blood 119

description: Alzheimer's disease sample

value: Alzheimer's disease


title: PCA.296: prostate_cancer_primary_296


title: PCA.294: prostate_cancer_primary_294


title: PCA.295: prostate_cancer_primary_295


title: SPJ1577_wt_rep1_RNA

description: rRNA-depleted RNA


title: CS2354_nht1_rep1_RNA

description: rRNA-depleted RNA


title: PCA.293: prostate_cancer_primary_293


title: Genomic DNA from blood 117

description: mild cognitive impairment sample

value: Included


title: Genomic DNA from blood 118

description: mild cognitive impairment sample


title: Genomic DNA from blood 121

description: Alzheimer's disease sample


title: CS1446_iec5_Input

data_processing:
Sequencing reads were de-multiplexed and aligned to the S. pombe reference genome, obtained from Pombase (Lock et al. 2019) with Bowtie using default parameters (Langmead et al. 2009). Genome-wide coverage was calculated with deepTools2 (Ramirez et al. 2016) and normalized to counts per million (CPM).
MNase-seq reads of each sample were mapped to the genome assembly of Schizosaccharomyces pombe using HISAT2 (v2.1.0). Potential PCR duplicates were removed using the function "MarkDuplicates" of Picard (v2.22.0, REMOVE_DUPLICATES=true). The fragment size distribution was measured by the function "CollectInsertSizeMetrics" of Picard (v2.22.0). Only mono-nucleosome sized fragments (<200 bp) were used for the downstream analysis.
Genome_build: ASM294v2
Supplementary_files_format_and_content: Genome-wide coverage calculated by deepTools2, normalized to CPM, in bigWig format

extract_protocol:
ChIP-seq: Log-phase yeast cells were crosslinked with 1% formaldehyde for 20 minutes with shaking at room temperature, followed by 5 minutes quenching with 125mM glycine. Cells were harvested, washed with PBS (phosphate-buffered saline), and resuspended in 100 ul ChIP lysis buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1% Triton X-100, 0.1% Deoxycholate, 1mM PMSF). 200 ul ice-cold glass beads were added and the mixtures were vigorously disrupted in a bead-beater with four 30 s rounds. The lysates were collected, to which 400 ul NP buffer was added (10 mM Tris, pH 7.4, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl 2 , 1 mM CaCl 2 ). MNase was added to the reaction and the reactions were incubated at 37°C for 20 minutes. MNase amount was titrated empirically so that the chromatin was digested to yield mainly mono- and di-nucleosomes. The reaction was stopped by adding 12 µl 0.5 M EDTA and the tubes were placed on ice. 100 µl 5X ChIP lysis buffer was added to the reaction, mixed by short vortexing, and the tubes were incubated on ice for 30 minutes. The reactions were then cleared by centrifugation at 16,000 x g for 10 minutes. 20 µl of the cleared supernatant was reserved as input and the rest used for immunoprecipitation.The cleared cell lysates were incubated with H3K9me2 antibody overnight at 4°C. The beads were then washed with ChIP lysis buffer twice, ChIP lysis buffer containing 0.5 M NaCl, Wash buffer (10 mM Tris, pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% Deoxycholate, 1 mM EDTA), and TE (50 mM Tris pH 8.0, 1 mM EDTA). The bound chromatin fragments were eluted with TES (50 mM Tris pH 8.0, 1 mM EDTA, 1% SDS) and the crosslinking was reversed by incubating at 65°C overnight. The protein DNA mixture was then subjected to proteinase K treatment and phenol:chloroform extraction before the DNA was precipitated by ethanol.   MNase-seq:MNase-seq sample preparation was the same as the ChIP-seq except that MNase was titrated to yield mainly mononucleosomes (~80% mono-nucleosomes) and the immunoprecipitation step was omitted.
ChIP-seq: 5-10 ng of ChIP and input DNA were used for library construction using the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, NEB). Mnase-seq:100 ng of extracted DNA was used for library construction as above.
ChIP-seq and Mnase-seq


title: PCA.292: prostate_cancer_primary_292


title: CS1446_iec5_H3K9me2

tag: antibody


title: Genomic DNA from blood 114

description: Alzheimer's disease sample


title: PCA.291: prostate_cancer_primary_291

tag: inflammation signature


title: Genomic DNA from blood 111

description: Alzheimer's disease sample


title: Genomic DNA from blood 113

description: mild cognitive impairment sample


title: SPJ649_wt_Input


title: PCA.290: prostate_cancer_primary_290

tag: ifng signature


title: SPJ649_wt_H3K9me2


title: PCA.289: prostate_cancer_primary_289

value: Black

tag: igg production


title: CS2370_iec5_rep2_MNase


title: Genomic DNA from blood 107

description: mild cognitive impairment sample


title: Genomic DNA from blood 110

description: mild cognitive impairment sample


title: CS2379_iec1_rep2_MNase


title: Genomic DNA from blood 108

description: control sample


title: Genomic DNA from blood 112

description: control sample


title: Genomic DNA from blood 120

description: mild cognitive impairment sample


title: PCA.286: prostate_cancer_primary_286

value: No

tag: nk activity


title: PCA.288: prostate_cancer_primary_288


title: PCA.287: prostate_cancer_primary_287


title: Genomic DNA from blood 109

description: mild cognitive impairment sample

tag: tissue

value: Male


title: Genomic DNA from blood 106

description: control sample

tag: age


title: Genomic DNA from blood 100

description: mild cognitive impairment sample


title: Genomic DNA from blood 116

description: mild cognitive impairment sample


title: CS2354_nht1_rep2_MNase


title: Genomic DNA from blood 103

description: Alzheimer's disease sample


title: SPJ1577_wt_rep2_MNase


title: Genomic DNA from blood 101

description: Alzheimer's disease sample


title: PCA.285: prostate_cancer_primary_285

tag: race


title: Genomic DNA from blood 105

description: control sample


title: Genomic DNA from blood 96

description: control sample


title: PCA.284: prostate_cancer_primary_284

tag: palsma cell content


title: Genomic DNA from blood 98

description: control sample


title: CS2370_iec5_rep1_MNase

tag: genotype


title: Genomic DNA from blood 99

description: Alzheimer's disease sample


title: PCA.283: prostate_cancer_primary_283


title: Genomic DNA from blood 104

description: Alzheimer's disease sample


title: CS2354_nht1_rep1_MNase

tag: media


title: PCA.282: prostate_cancer_primary_282


title: PCA.281: prostate_cancer_primary_281


title: Genomic DNA from blood 97

description: mild cognitive impairment sample

tag: Sex


title: SPJ1577_wt_rep1_MNase


title: Genomic DNA from blood 102

description: Alzheimer's disease sample

tag: disease state


title: Genomic DNA from blood 92

description: control sample

tag: disease state2


title: Genomic DNA from blood 93

description: Alzheimer's disease sample


title: PCA.279: prostate_cancer_primary_279

tag: psa


title: PCA.280: prostate_cancer_primary_280

tag: grade group

value: Yes


title: Genomic DNA from blood 94

description: Alzheimer's disease sample


title: M_tick3

city: Urumqi

first: Ercha

last: Hu

state: Xinjiang

address: Nongda east Rd311

department: College of Veterinary

institute: Xinjiang Agricultural University

description:
pooled sample of 5 ticks
gene_expression.txt
Trinity.gene.fasta

data_processing:
Illumina Casava1.8 software used for basecalling.
Firstly, Cutadapt 2.6 was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases;
Then denovo assembly of the transcriptome was performed with Trinity , and salmon was used to perform expression level for unigenes by calculating TPM;
All assembled unigenes were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/),Gene ontology (GO) (http://www.geneontology.org), SwissProt (http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.genome.jp/kegg/), Protein family (Pfam) (http://pfam.xfam.org/) and eggnog (http://eggnogdb.embl.de/) databases using DIAMOND with a threshold of E value < 0.00001.
Supplementary_files_format_and_content: tab-delimited text file include TPM values and fasta file including all trinity gene sequences

organism: Dermacentor marginatus

source_name: Whole body of the tick

extract_protocol:
Ticks were pulverized in liquid nitogen, then total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Poly(A) RNA was purified from total RNA(5ug) using poly-T oligo-attached magnetic beads by two rounds of purification. Then the left RNA was fragmented into small pieces using divalent cations under elevated temperature.The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina, San Diego, USA).

tag: state

value: newly molted for 5 days

tag: tick strain

value: laboratory reared F2 generation

value: female

value: adult


title: Genomic DNA from blood 87

description: mild cognitive impairment sample

value: mild cognitive impairment

value: mild cognitive impairment stable


title: Genomic DNA from blood 91

description: Alzheimer's disease sample


title: Genomic DNA from blood 89

description: control sample

value: control


title: M_tick2


title: Genomic DNA from blood 95

description: control sample


title: Genomic DNA from blood 90

description: Alzheimer's disease sample


title: PCA.278: prostate_cancer_primary_278

value: White

tag: non-organ confined

tag: inflammation signature


title: M_tick1


title: H_tick3

value: unfed for 6 months


title: PCA.277: prostate_cancer_primary_277

tag: ifng signature

tag: igg production


title: CS2379_iec1_rep1_MNase

value: YEA


title: Genomic DNA from blood 86

description: control sample

tag: tissue

value: whole blood

value: Female

value: Excluded


title: H_tick2

tag: age


title: Genomic DNA from blood 88

description: mild cognitive impairment sample

value: mild cognitive impairment to alzheimer's disease converter

value: Included


title: Genomic DNA from blood 82

description: Alzheimer's disease sample

value: Alzheimer's disease


title: H_tick1


title: PCA.275: prostate_cancer_primary_275

tag: race

value: Yes

tag: nk activity


title: PCA.276: prostate_cancer_primary_276

value: No

tag: palsma cell content


title: PCA.274: prostate_cancer_primary_274

value: Black


title: Genomic DNA from blood 78

description: mild cognitive impairment sample

value: Male


title: Genomic DNA from blood 84

description: Alzheimer's disease sample


title: F_tick3

description:
pooled sample of 3 ticks
gene_expression.txt
Trinity.gene.fasta

value: feed on Equus caballus blood for 7 days

tag: treatment

value: 24 h after detechment from host

value: laboratory reared F2 generation

value: female

value: adult


title: Genomic DNA from blood 115

description: mild cognitive impairment sample

tag: Sex

value: mild cognitive impairment


title: Genomic DNA from blood 80

description: Alzheimer's disease sample

tag: disease state


title: Genomic DNA from blood 81

description: mild cognitive impairment sample

tag: disease state2

value: mild cognitive impairment stable


title: Genomic DNA from blood 83

description: control sample

value: whole blood

value: control


title: PCA.273: prostate_cancer_primary_273

tag: psa

value: White


title: Genomic DNA from blood 79

description: Alzheimer's disease sample

value: Female


title: F_tick2


title: Genomic DNA from blood 85

description: mild cognitive impairment sample

value: Included


title: Genomic DNA from blood 77

description: Alzheimer's disease sample

value: Alzheimer's disease


title: Genomic DNA from blood 74

description: control sample


title: Genomic DNA from blood 76

description: Alzheimer's disease sample


title: F_tick1


title: PCA.272: prostate_cancer_primary_272

tag: grade group


title: Genomic DNA from blood 75

description: control sample


title: Genomic DNA from blood 70

description: Alzheimer's disease sample


title: PCA.271: prostate_cancer_primary_271


title: Genomic DNA from blood 72

description: control sample


title: Genomic DNA from blood 68

description: mild cognitive impairment sample

value: mild cognitive impairment to alzheimer's disease converter


title: Genomic DNA from blood 65

description: Alzheimer's disease sample


title: Genomic DNA from blood 69

description: Alzheimer's disease sample


title: Genomic DNA from blood 67

description: mild cognitive impairment sample

value: Excluded


title: PCA.269: prostate_cancer_primary_269

value: Yes


title: Genomic DNA from blood 71

description: Alzheimer's disease sample

value: Male


title: PCA.266: prostate_cancer_primary_266

value: Black

value: No


title: Genomic DNA from blood 73

description: control sample


title: Genomic DNA from blood 64

description: mild cognitive impairment sample


title: Genomic DNA from blood 62

description: control sample


title: PCA.268: prostate_cancer_primary_268


title: PCA.267: prostate_cancer_primary_267


title: LCC2, biological rep3 [circRNA]

description:
TAM-4
circRNA expression data from LCC2 cells.

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized in an Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and GeneSpring software was used to analyze the raw data, which are normalized by quantile normalization.

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: cell line

tag: tamoxifen resistance

value: tamoxifen-resistant

tag: fulvestrant resistance


title: PCA.265: prostate_cancer_primary_265

tag: non-organ confined

tag: inflammation signature


title: Genomic DNA from blood 59

description: control sample


title: LCC2, biological rep1 [circRNA]

description:
TAM-2
circRNA expression data from LCC2 cells.


title: LCC2, biological rep2 [circRNA]

description:
TAM-3
circRNA expression data from LCC2 cells.


title: Genomic DNA from blood 63

description: mild cognitive impairment sample

value: unknown


title: PCA.264: prostate_cancer_primary_264

tag: ifng signature

tag: igg production


title: Genomic DNA from blood 55

description: mild cognitive impairment sample

tag: tissue

tag: age


title: Genomic DNA from blood 60

description: Alzheimer's disease sample


title: PCA.270: prostate_cancer_primary_270

tag: race

tag: nk activity


title: Genomic DNA from blood 61

description: Alzheimer's disease sample


title: Genomic DNA from blood 58

description: control sample


title: MCF-7, biological rep3 [circRNA]

description:
S-6
circRNA expression data from MCF-7 cells.


title: Genomic DNA from blood 57

description: control sample


title: Genomic DNA from blood 54

description: mild cognitive impairment sample


title: PCA.263: prostate_cancer_primary_263

tag: palsma cell content


title: Genomic DNA from blood 66

description: mild cognitive impairment sample

tag: Sex


title: MCF-7, biological rep2 [circRNA]

description:
S-5
circRNA expression data from MCF-7 cells.


title: Genomic DNA from blood 51

description: mild cognitive impairment sample

tag: disease state


title: PCA.262: prostate_cancer_primary_262


title: LCC9, biological rep3 [circRNA]

description:
FUL-5
circRNA expression data from LCC9 cells.

value: fulvestrant-resistant


title: Genomic DNA from blood 52

description: control sample

tag: disease state2