title: Flt-1+/- (VR1+/-)-RNA Seq 3

status: Public on Jun 30 2019

type: SRA

city: Charlottesville

first: Vijay

middle: C

last: Ganta

state: VA

address: 454 Farrish Cir, Apt 3

country: USA

institute: University of Virginia

library_source: transcriptomic

data_processing:
The barcoded libraries were sequenced on an Illumina NextSeq 500 using 150-cycle High Output Kits (Illumina)
A minimum of 15 million paired-end (2 x 75 bp) sequence reads were generated per sample. Quality control of the resulting sequence data was performed using FastQC (http://www. Bioinformatics.babraham.ac.uk/projects/fastqc).  All data were analyzed using Illumina BaseSpace applications. Sequencing reads were aligned to the mouse mm10 reference transcriptome and using the TopHat Alignment v1.0.0 application
Expression values (FPKM; Fragments Per Kilobase of transcript per Million mapped reads) were then generated for each gene and differentially expressed genes (at a false discovery rate (FDR) of < 0.05) were identified using Cufflinks Assembly and Differential Expression v1.1.0 application.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

molecule: total RNA

organism: Mus musculus

growth_protocol: Bone marrow from C57BL/6 mice legs was isolated using 10ml syringe fitted with a 26 gauze  needle and PBS. Bone marrow was passed through a 70 micron filters and cultured in RPMI supplemented with 10% FCS and 10% L292 conditioned medium. Media was changes every 2 days. At day 7, macrophage differentiation was confirmed visually using a bright field microscope.

extract_protocol:
BMDMs were lysed in Trizol reagent and RNA isolated using Ambion total RNA isolation kits. RNA-seq libraries were constructed from 500 ng of total RNA using the TruSeq Stranded Total RNA prep kit (Illumina, San Diego, CA). This kit enriches for RNA species of interest, mRNA and long non-polyadenylated RNAs, by depleting cytoplasmic rRNAs
Standard Illumina protocols were used to prepare RNA libraries for sequencing

treatment_protocol: Bone marrow derived macrophages at day 7 in culture were washed once with PBS and incubated in fresh culture medium under regular growth conditions (5% CO2) or incubated in starvation medium and kept in hypxia chamber (2% O2) for 6h.

tag: strain background

tag: genotype/variation

tag: cell type

value: primary bone marrow derived macrophages (BMDM)


title: Flt-1+/- (VR1+/-)-RNA Seq 2


title: Flt-1+/+ (VR1+/+)-RNA Seq 2


title: Flt-1+/+ (VR1+/+)-RNA Seq 3


title: AT3_macrophage_2

city: Houston

first: Ik Sun

last: Kim

state: TX

address: 1 Baylor Plaza

department: Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

description: processed data column: m.6_S11.MAT3_21

data_processing:
Illumina Nextseq 500 automatically used bcl2fastq2 (version 2.17) for basecalling.
The pair-ended reads were mapped to the mouse genome (UCSC mm10) using STAR_2.4.2a with NCBI RefSeq genes as the reference.
The read counts generated by STAR were used as the raw gene expression values.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample.

source_name: AT3 tumor-associated macrophage

extract_protocol:
To obtain tumor-associated neutrophils and macrophages, tumors were dissociated into single cell suspension according to the protocol of Tumor Dissociation Kit, mouse (Miltenyi Biotec). Cell sorting was performed using Aria1 cell sorter (BD Bioscience) based on the following gating strategy: DAPI- CD45+ CD11b+ Ly6G+ Ly6C med-low for neutrophils, DAPI- CD45+ CD11b+ Ly6G- Ly6C- F4/80+ for macrophages. Myeloid cells were sorted directly into TRIzol LS and were frozen at -80C till further processing. RNA was extracted using Direct-zol RNA microprep kit (Zymo).
RNA libraries were prepared for sequencing using protocol reported in Sheng et al, Nature Methods 14, 267–270 (2017)

value: macrophage

tag: experimental system

value: in vivo

tag: passsage

tag: strain


title: AT3_macrophage_1

description: processed data column: m.2_S10.MAT3_20


title: AT3_macrophage_3

description: processed data column: m.7_S12.MAT3_22


title: Flt-1+/+ (VR1+/+)-RNA Seq 1


title: E0771_macrophage_3

description: processed data column: m.3_S15.ME0771_25

source_name: E0771 tumor-associated macrophage


title: E0771_macrophage_2

description: processed data column: m.2_S14.ME0771_24


title: Flt-1+/- (VR1+/-)-RNA Seq 1


title: E0771_neutrophil_1

description: processed data column: n.1_S16.NE0771_26

source_name: E0771 tumor-associated neutrophil

value: neutrophil

value: BALB/C


title: E0771_neutrophil_2

description: processed data column: n.2_S17.NE0771_27


title: 2208L_macrophage_2

description: processed data column: m.10_S2.M2208L_11

source_name: 2208L tumor-associated macrophage


title: 2208L_macrophage_3

description: processed data column: m.11_S3.M2208L_12


title: T11_macrophage_1

description: processed data column: m.6_S19.MT11_29

source_name: T11 tumor-associated macrophage


title: AT3_neutrophil_3

description: processed data column: n.7_S9.NAT3_04

source_name: AT3 tumor-associated neutrophil


title: E0771_neutrophil_3

description: processed data column: n.3_S18.NE0771_28


title: 2208L_macrophage_1

description: processed data column: m.1_S1.M2208L_09


title: T11_macrophage_3

description: processed data column: m.8_S21.MT11_31


title: T11_macrophage_2

description: processed data column: m.7_S20.MT11_30


title: AT3_neutrophil_1

description: processed data column: n.2_S7.NAT3_02


title: AT3_neutrophil_2

description: processed data column: n.6_S8.NAT3_03


title: 2208L_neutrophil_3

description: processed data column: n.11_S6.N2208L_17

source_name: 2208L tumor-associated neutrophil


title: 2208L_neutrophil_1

description: processed data column: n.1_S4.N2208L_14


title: T11_neutrophil_3

description: processed data column: n.8_S24.NT11_34

source_name: T11 tumor-associated neutrophil


title: E0771_macrophage_1

description: processed data column: m.1_S13.ME0771_23


title: 2208L_neutrophil_2

description: processed data column: n.10_S5.N2208L_16


title: T11_neutrophil_2

description: processed data column: n.7_S23.NT11_33


title: T11_neutrophil_1

description: processed data column: n.6_S22.NT11_32


title: AT3_cancer_3

source_name: AT3 breast cancer cell line

growth_protocol: Cells were cultured in DMEM/High Glucose Medium (HyClone). Media contained 10% FBS (Sigma), 100U/ml penicillin, 100ug/ml streptomycin (Lonza), and 250ng/ml amphotericin B (Lonza). For RNA extraction, cells were plated in 6 well plate with seeding density of 0.3 X 10^6.

extract_protocol:
Total RNA was extracted using Direct-zol RNA miniprep kit (Zymo), except that TRIzol LS (invitrogen) was used instead of TRI reagent.
RNA libraries were prepared for sequencing using protocol reported in Sheng et al, Nature Methods 14, 267–270 (2017)

value: cancer cell

value: in vitro


title: AT3_cancer_1


title: AT3_cancer_2


title: E0771_cancer_2

source_name: E0771 breast cancer cell line

growth_protocol: Cells were cultured in RPMI 1640 medium (HyClone, supplemented with 10mmol/L HEPES(Gibco)). Media contained 10% FBS (Sigma), 100U/ml penicillin, 100ug/ml streptomycin (Lonza), and 250ng/ml amphotericin B (Lonza). For RNA extraction, cells were plated in 6 well plate with seeding density of 0.3 X 10^6.


title: PyMT-N_cancer_2

source_name: PyMT-N breast cancer cell line


title: PyMT-N_cancer_3


title: PyMT-N_cancer_1


title: T11_cancer_2

source_name: T11 breast cancer cell line


title: PyMT-M_cancer_2

source_name: PyMT-M breast cancer cell line


title: 4T1_cancer_3

source_name: 4T1 breast cancer cell line


title: 67NR_cancer_2

source_name: 67NR breast cancer cell line


title: T11_cancer_3


title: T11_cancer_1


title: 4T1_cancer_1


title: 2208L_cancer_1

source_name: 2208L breast cancer cell line


title: 4T1_cancer_2


title: E0771_cancer_1


title: 2208L_cancer_2


title: PyMT-M_cancer_3


title: E0771_cancer_3


title: 67NR_cancer_3


title: 67NR_cancer_1


title: UBE3A_null_input_2

city: Madison

first: Carissa

middle: L

last: Sirois

state: WI

address: 1500 Highland Ave T515

department: Waisman Center

institute: University of Wisconsin-Madison

library_source: genomic

data_processing:
Align to genome using bowtie2: Vesion 2.2.9
Sort with samtools: Version 1.7
Index with samtools: Version 1.7
Convert to tag align format for size estimation: PhantompeakqualTools
Peak calling with MACS2: Version 2.1.2
ENCODE IDR analysis pipeline: https://github.com/nboley/idr/archive/2.0.0.tar.gz
Genome_build: hg19
Supplementary_files_format_and_content: bigBed for peak calls: bigWig for p-value ChIP-Seq Signals

molecule: genomic DNA

organism: Homo sapiens

source_name: hESCs

growth_protocol: hESCs were grown and maintained as previously described (Chamberlain SJ, et al. (2010), Proc Natl Acad Sci U S A 107(41):17668-17673); hESC-derived neural progenitors and neurons were differentiated as previously described (Germain, ND, et al. (2014) Mol Autism 5:44)

extract_protocol:
hESCs, NPCs, and neurons were processed for ChIP-seq as previously described (Cotney & Noonan (2015), Cold Spring Harb Protoc 2015(4): 419
Libraries were prepared from ChIPed DNA using the Takara ThruPLEX DNA-seq library preparation kit according to manufacturer's instructions. Libraries were quantified with the NEBNext Library Quant Kit for Illumina

treatment_protocol: UBE3A-null hESCs were obtained by editing H9 hESCs with CRISPR sgRNAs

value: H9 hESCs with homozygous UBE3A deletion

tag: weeks of differentiation

value: no differentiation

tag: genotype

value: UBE3A KO

tag: antibody

value: none (input)

tag: antibody catalog number and manufacturer


title: 2208L_cancer_3


title: UBE3A_null_input_1


title: H9_Neuron_input_1

source_name: Neurons

value: H9 hESC-derived neurons

value: 10 weeks

value: wildtype


title: PyMT-M_cancer_1


title: H9_NPC_input_2

source_name: Neural progenitor cells

value: H9 hESC-derived neural progenitors

value: 5 weeks


title: H9_NPC_input_1


title: SB_230

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
Data quality was assessed using fastqc (0.10.1)
Sequential alignments against reference databases was conducted using bowtie 2 (2.2.6)
file converstions were performed using samtools (1.2)
Reference for microRNA annotations was miRBase version 20 (http://www.mirbase.org)
Genome_build: GRCh37
Supplementary_files_format_and_content: the raw read count for microRNAs annotated in miRBase version 20. One row per microRNA (total 2578), one column per sample (total 48).
Supplementary_files_format_and_content: tags per million total reads (per lane) for microRNAs annotated in miRBase version 20. One row per microRNA (total 2578), one column per sample (total 48).

source_name: case_CTAD Plasma

extract_protocol:
The miRNeasy Mini Kit (Qiagen, Germany) was applied to isolate total RNA, including small RNAs, from plasma. Frozen plasma samples were thawed at room temperature and centrifuged at 12 000 g for 5 minutes to separate potential debris from cell-free component. 200 µl of plasma were mixed by vortexing with 1 ml Qiazol containing a mix of three synthetic spike-in controls (Exiqon, Denmark). Following incubation at room temperature for 10 minutes, 200 µl chloroform were added and vigorously mixed by vortexing. After centrifugation at 12 000 g for 15 minutes at 4°C, 650 µl of aqueous phase were aspirated. Glycogen (Ambion, USA) was added to a final concentration of 50 µg/ml. Samples were then transferred to silica columns and further processed using the QIAcube liquid handling robot according to the manufacturer’s protocol. RNA was precipitated with 750 µl Ethanol, triple washed with RPE-buffer, followed by RNA-elution in 30 µl nuclease free water and stored at –80°C.
Small RNA sequencing libraries were generated using the CleanTag SmallRNA library preparation kit (TriLink, USA) according to the manufacturer’s recommendations. Two µl total RNA were used for sequential 3’ and 5’ adapter ligation at 28°C for 1 hour, followed by 65°C for 20 minutes. Adapters were prediluted 1:12 to account for low RNA abundance. Reverse transcription was performed at 50°C for 1 hour. PCR amplification was performed using barcoded Illumina primers for small RNA sequencing: 26 cycles of denaturation (98°C, 10s), annealing (60°C, 30s) and elongation (72°C, 15s) were used. PCR products were purified using the QiaQuick protocol (Qiagen, Germany), and size checked by capillary electrophoresis using the DNA 1000 Chip (Agilent, USA). The ~145bp peak concentration was used as a basis for pooling equimolar amounts of DNA. The pool was gel purified to select for template inserts between 18 and 50 bp.

tag: subject status

value: patient with post-operative liver dysfunction

tag: cancer type

value: HCC

tag: tissue

value: CTAD Plasma


title: SB_71

source_name: control_CTAD Plasma

value: patient without post-operative liver dysfunction

value: CCC


title: SB_72


title: SB_154


title: SB_20


title: H9_Neuron_input_2


title: SB_149

value: mCRC


title: SB_110


title: SB_73


title: SB_136


title: SB_161


title: SB_183


title: SB_63


title: SB_107


title: SB_134


title: SB_124


title: SB_145


title: SB_17


title: SB_150


title: SB_153


title: SB_54


title: SB_186


title: SB_184


title: SB_162


title: SB_19


title: SB_191


title: SB_50


title: SB_125


title: SB_137


title: SB_173


title: SB_140


title: SB_128


title: SB_175


title: SB_108


title: SB_167


title: SB_80


title: SB_39


title: SB_159


title: SB_102


title: OAW42_RNA-Seq

city: Los Angeles

first: Michelle

middle: Renee

last: Jones

state: CA

address: 8720 Alden Dv

department: Biomedical Sciences

institute: Cedars-Sinai Medical Center

data_processing:
Pre-alignment QC was performed using FastQC (v0.11.5) and fastqscreen (v0.6.3) and results visualized in MultiQC (v1.3).
Reads were aligned with STAR (v2.5.1b) to Gencode v26 (hg38 build of the human reference genome).
featureCounts function of the subread package (v1.5.2) was used to count the number of reads mapping to each gene in Gencode v36, collapsing all exons from a gene into a single feature.
Genome_build: hg38
Supplementary_files_format_and_content: csv file with raw read count

molecule: polyA RNA

growth_protocol: Commerically available cell lines were maintained according to recommended condition by the supplier (ATCC). In house cell lines (iOSE and FTSEC) were grown in DMEM media, with iOSE supplemented with 10FBS and FTSEC supplemented with 2% Ultroser G (Pall Corporation). Cell lines were passaged and plated into 150mm plates. Cells were harvested at ~80% confluency and spun down, pellets were suspended and stored in Buffer RLT or QIAzol reagent (Qiagen, MD).

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen, MD) as per manufacturer’s instructions.
Total RNA were used as template for cDNA libraries and were prepared as poly-A selected libraries using the TruSeq v2 protocol (Illumina, San Diego, CA). Each library was pooled and the pool was sequenced across 4 lanes on the Illumina HiSeq4000 in 2 × 75bp format for a minimum of XGB per sample, representing an average of 33.4M reads. FTSEC lines were sequenced separately in a previous experiment, in 1 x 75bp format by the University of Southern California Epigenome Core Facility.

value: Model of High Grade Serous Ovarian Cancer from metastatic (ascites) sample

tag: cell line


title: SB_181


title: SB_187


title: SB_56


title: SB_139


title: CaOV3_RNA-Seq

value: Model of High Grade Serous Ovarian Cancer


title: SB_23


title: RMGII_RNA-Seq

source_name: RMG-II

value: Model of Clear Cell Ovarian Cancer

value: RMG-II


title: BT549_RNA-Seq

value: Model of Triple Negative Breast Cancer


title: Kuramochi_RNA-Seq

source_name: Kuramochi

value: Kuramochi


title: ES2_RNA-Seq


title: HeyA8_RNA-Seq


title: GTFR230_RNA-Seq

value: Model of mucinous Ovarian Cancer


title: JHOC5_RNA-Seq


title: EEC116_RNA-Seq

value: Endometriosis


title: SB_117


title: SB_180


title: SB_156


title: IOSE4_RNA-Seq

value: TERT immortalized ovarian surface epithelial cell line


title: UWB1.289_RNA-Seq


title: IOSE11_RNA-Seq


title: MCF7_RNA-Seq

value: Model of Breast Cancer (derived from metastatic plueral effusion)


title: EFO27_RNA-Seq

value: Model of Mucinous Ovarian Cancer


title: MCAS_RNA-Seq

source_name: MCAS

value: MCAS


title: prostate tumour CPCG0395

type: RNA

city: Toronto

first: Yu-Jia

last: Shiah

state: Ontario

address: MaRS Centre 661 University Avenue Suite 510

department: Informatics and Bio-computing

country: Canada

institute: Ontario Institute for Cancer Research

description: new

hyb_protocol: 500 ng of labeled cRNA was hybridized to Hugene2.0 and HTA2.0 according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol

data_processing: All mRNA analysis was performed using R (v3.4.3). Background correction and normalization algorithms were implemented in the modified affy (v1.48.0) package downloaded from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp. The Robust multichip average (RMA) algorithm was applied to the raw intensity data. Probes were mapped to Entrez gene ID using custom CDF files (v18) for HTA 2.0 and HuGene 2.0 ST array.  The sva package (v3.24.4) was used to correct for batch effects between different arrays.

label: biotin

source_name: Fresh frozen prostate tumour

label_protocol: Affymetrix protocol

extract_protocol: Total RNA was extracted from alternating adjacent sections, using the mirVana miRNA Isolation Kit (Life Technologies), according to the manufacturer’s instructions.

value: prostate tumour

value: intermediate

tag: disease state

value: Sporadic

tag: batch


title: prostate tumour CPCG0396

description: new


title: prostate tumour CPCG0398

description: new


title: prostate tumour CPCG0415

description: new


title: prostate tumour CPCG0266

description: re-analysis of GSM2226267


title: prostate tumour CPCG0346

description: re-analysis of GSM2226269


title: prostate tumour CPCG0334

description: re-analysis of GSM2226268


title: prostate tumour CPCG0416

description: new


title: MCF10A_RNA-Seq

value: Model of Normal Breast Epithelium


title: prostate tumour CPCG0414

description: re-analysis of GSM2226265

value: low


title: prostate tumour CPCG0413

description: re-analysis of GSM2226264


title: prostate tumour CPCG0408

description: new

value: high


title: prostate tumour CPCG0409

description: re-analysis of GSM2226260


title: prostate tumour CPCG0411

description: re-analysis of GSM2226262


title: prostate tumour CPCG0407

description: re-analysis of GSM2226259


title: prostate tumour CPCG0401

description: re-analysis of GSM2226258


title: prostate tumour CPCG0382

description: new


title: prostate tumour CPCG0361

description: re-analysis of GSM2226270


title: prostate tumour CPCG0391

description: re-analysis of GSM2226257


title: prostate tumour CPCG0387

description: re-analysis of GSM2226256


title: prostate tumour CPCG0378

description: re-analysis of GSM2226254


title: prostate tumour CPCG0241

description: re-analysis of GSM2226266


title: prostate tumour CPCG0373

description: re-analysis of GSM2226252


title: prostate tumour CPCG0372

description: re-analysis of GSM2226251


title: prostate tumour CPCG0371

description: re-analysis of GSM2226250


title: prostate tumour CPCG0365

description: re-analysis of GSM2226248


title: prostate tumour CPCG0412

description: re-analysis of GSM2226263


title: prostate tumour CPCG0357

description: re-analysis of GSM2226243


title: prostate tumour CPCG0410

description: re-analysis of GSM2226261


title: prostate tumour CPCG0363

description: re-analysis of GSM2226246


title: prostate tumour CPCG0358

description: re-analysis of GSM2226244


title: prostate tumour CPCG0356

description: re-analysis of GSM2226242


title: prostate tumour CPCG0354

description: re-analysis of GSM2226240


title: prostate tumour CPCG0353

description: re-analysis of GSM2226239


title: prostate tumour CPCG0352

description: re-analysis of GSM2226238


title: prostate tumour CPCG0350

description: re-analysis of GSM2226237


title: prostate tumour CPCG0349

description: new


title: prostate tumour CPCG0375

description: re-analysis of GSM2226253


title: prostate tumour CPCG0342

description: re-analysis of GSM2226234


title: prostate tumour CPCG0348

description: re-analysis of GSM2226236


title: prostate tumour CPCG0341

description: re-analysis of GSM2226233


title: prostate tumour CPCG0340

description: re-analysis of GSM2226232


title: prostate tumour CPCG0381

description: re-analysis of GSM2226255


title: prostate tumour CPCG0344

description: re-analysis of GSM2226235


title: SB_219

value: patient with post-operative liver dysfunction

value: mCRC

value: CTAD Plasma


title: prostate tumour CPCG0339

description: re-analysis of GSM2226231


title: SB_37

value: HCC


title: prostate tumour CPCG0364

description: re-analysis of GSM2226247


title: prostate tumour CPCG0366

description: re-analysis of GSM2226249


title: prostate tumour CPCG0362

description: re-analysis of GSM2226245


title: prostate tumour CPCG0335

description: new


title: prostate tumour CPCG0331

description: re-analysis of GSM2226229


title: prostate tumour CPCG0355

description: re-analysis of GSM2226241


title: prostate tumour CPCG0269

description: re-analysis of GSM2226227


title: prostate tumour CPCG0324

description: re-analysis of GSM2226228


title: prostate tumour CPCG0267

description: re-analysis of GSM2226226


title: prostate tumour CPCG0265

description: re-analysis of GSM2226225


title: prostate tumour CPCG0262

description: re-analysis of GSM2226223


title: prostate tumour CPCG0258

description: re-analysis of GSM2226221


title: prostate tumour CPCG0249

description: re-analysis of GSM2226218


title: prostate tumour CPCG0250

description: re-analysis of GSM2226219


title: prostate tumour CPCG0248

description: re-analysis of GSM2226217


title: prostate tumour CPCG0246

description: re-analysis of GSM2226216


title: prostate tumour CPCG0236

description: re-analysis of GSM2226215


title: ref2-1 med5a-1 med5b-1 rep2

city: West Lafayette

first: Clint

last: Chapple

state: IN

address: 175 S. University St.

department: Department of Biochemistry

institute: Purdue University

data_processing:
Casava1.8.2 software was used for basecalling.
Trimmomatic and/or fastx_clipper were used to remove adapters. Poor quality bases (less than Phred-20) were removed (clipped) from both the 5' and 3' ends of the Unaligned reads. After adapter removal and quality clipping any reads below a minimum (30 bases) length were discarded. Reads were then mapped to TAIR10 assembly of the Arabidopsis genome using Tophat v2.1.0 with default parameters.
Digital gene expression (counts) was determined for each sample using HTSeq-count v0.6.1 (Anders et al., 2015) with the following parameters: -s reverse -r pos -m intersection-nonempty -t exon -i gene_id.
Differential expression analysis was performed using the edgeR package as follows: edgeR analysis began with a count table comprising 33,602 genes. Genes expressed at low levels were then filtered out by removing any genes for which there was not at least 1 count per million in at least four of the samples. This resulted in a list of 18,842 expressed genes. Counts were then normalized using TMM normalization. Next, the “ANOVA-like” procedure in EdgeR was used to identify genes that were differentially expressed between any of the genotypes (FDR < 0.05). This resulted in a list of 14,688 differentially expressed genes. To determine which of these genes were differentially expressed in each of the mutants compared to wild type, the exact test for the negative binomial distribution (Robinson and Smyth, 2008) was used followed by a Bonferroni correction to maintain a gene-wise error rate of 0.05
Genome_build: TAIR10
Supplementary_files_format_and_content: Comma-separated values files include raw count values for each sample.

organism: Arabidopsis thaliana

source_name: Whole rosettes

growth_protocol: Seeds were sown nine per 4" x 4" pot and positions of the pots were randomized. Seeds were held at 4C for two days before transferring to 23C under a 16 hr light, 8 hr dark photoperiod. Material was harvested 6.5 hours after subjective dawn on the 18th day after transferring to the growth chamber.

extract_protocol:
For each sample, five whole rosettes were pooled from different pots and ground under liquid nitrogen. Approximately 100 mg of the ground tissue was used to extract total RNA using the Qiagen RNEasy Plant Mini kit (Cat#74904) with on-column DNAse treatment (Cat#79254). Total rRNA was then enriched for polyA+ RNA.
Illumina TruSeq Stranded mRNA Sample Prep Kit (Cat#RS-122-2103) was used with 2 ug of total RNA for the construction of dual barcoded sequencing libraries.

tag: ecotype

tag: age

value: 18 days

value: ref2-1 med5a-1 med5b-1

value: whole rosette


title: ref5-1 med5a-1 med5b-1 rep3

value: ref5-1 med5a-1 med5b-1


title: ref2-1 med5a-1 med5b-1 rep3


title: prostate tumour CPCG0336

description: re-analysis of GSM2226230


title: ref2-1 med5a-1 med5b-1 rep1


title: ref5-1 med5a-1 med5b-1 rep2


title: ref5-1 med5a-1 med5b-1 rep1


title: prostate tumour CPCG0333

description: new


title: med5a-1 med5b-1 rep2

value: med5a-1 med5b-1


title: ref2-1 rep2


title: med5a-1 med5b-1 rep1


title: ref2-1 rep3


title: ref5-1 rep3


title: prostate tumour CPCG0263

description: re-analysis of GSM2226224


title: ref2-1 rep1


title: ref5-1 rep1


title: wild type rep3

value: wild type


title: prostate tumour CPCG0260

description: re-analysis of GSM2226222


title: wild type rep1


title: wild type rep2


title: prostate tumour CPCG0255

description: re-analysis of GSM2226220


title: med5a-1 med5b-1 rep3


title: ref5-1 rep2


title: SH3_CD163

city: Warsaw

first: Bartosz

last: Wojtas

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

data_processing:
Basecalling with HCS 2.2.68
Bcl2fastq.gz processing of bcl files to fastq.gz
fastq.gz trimming for adapter contamination and low quality reads and aligned with tophat2 to rn5.fa reference
FPKM calculation with RSEM software using Ensembl transcriptome annotations for rn5.fa genome version
Genome_build: rn5
Supplementary_files_format_and_content: normalized abundance measurements

organism: Rattus norvegicus

source_name: sorted cells from brain after sham

extract_protocol:
We used CD163 as a marker of perivascular and meningeal macrophages in rats, whereas in mice CD206 and CD169 identify perivascular and meningeal macrophage population in the CNS.  In rats we found an accumulation of CD163+ perivascular and meningeal macrophages in response to cerebral ischemia, which tend to infiltrate in to the parenchymal lesion. RNA-sequencing of FACS sorted CD11b+CD163+ population revealed these cells are highly proliferative and express pro-inflammatory phenotype in the parenchyma
In total, 6 strand-specific RNA libraries for high-throughput sequencing were prepared (three biological replicates for each treatment) using the KAPA Stranded mRNA Sample Preparation Kit according to the manufacturer’s protocol. Briefly, the poly-A containing mRNA molecules were purified from 500ng of total RNA (extracted FACS sorted cells from the brain samples of sham operated and MCAo animals) using poly-T oligo-attached magnetic beads (Kapa Biosystems, MA, USA ) The mRNA was then fragmented and the first-strand cDNA was synthesized using reverse transcriptase and random hexamers. Second cDNA synthesis was performed by removing the RNA template and synthesizing a replacement strand, incorporating dUTP in place of dTTP, to generate double-stranded (ds) cDNA. dsDNA was then subjected to the addition of “A” bases to the 3′ ends and ligation of adapters from NEB followed by uracil digestion in a loop structure of adapter by USER enzyme from NEB (Ipswich, MA, USA). Amplification of fragments with adapters ligated on both ends was performed by PCR using primers containing Truseq barcodes from NEB (Ipswich MA, USA).

treatment_protocol: Focal cerebral ischemia was induced by transient occlusion of middle cerebral artery (MCA) as previously reported (Szydlowska, Zawadzka, & Kaminska, 2006; Zawadzka et al., 2012). Briefly, the rats were anesthetized using 1.5% isoflurane in oxygen and ischemia was produced by advancing the tip of a rounded 0.4 mm nylon suture (Doccol Co.) into the right internal carotid artery entering through the right external carotid artery. After 90 min of occlusion, the nylon filament was withdrawn to allow reperfusion. Throughout the surgery the animal’s core body temperature was maintained at 37±0.5°C with a thermostatically controlled heating pad. For the Sham operated animals the right common carotid artery was isolated and the external carotid artery was permanently ligated.

value: Wistar

tag: developmental stage

value: adult

value: brain

tag: treatment

value: sham

tag: cell markers


title: MCAO2_CD163

source_name: sorted cells from brain after MCAO

value: Rats were induced 90 min of transient MCAO


title: SH2_CD163


title: SH1_CD163


title: MCAO1_CD163


title: RNA-seq_ctrl_kd_rep1

city: Shanghai

first: Weisheng

last: Zheng

address: Siping Road, No.1239

department: Department of Bioinformatics

country: China

institute: Tongji University

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using hisat2 v2.1.0 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a in-house developed protocol. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted by featurecounts. The reads distribution was modeled by DESeq2 and then the unwanted variations were removed by RUVSeq by using the top 5000 non DE genes with highest pvalues as negtive contrl genes.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: Neuroblastoma cells

growth_protocol: Human neuroblastoma cell line BE(2)C cells were routinely cultured in DMEM(Life Technologies 11995065) supplemented with 10%FBS (foetal bovine serum) at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Next day, total RNA was extracted from the cells by using RNA extract tool-kit.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

treatment_protocol: ~4X105 cells were cultured in dish and incubated with siRNA（siRNA concentration=80nM） and Lipofectamine 2000 (Life Technologies 11668019) in Optimem (Life Technologies 51985034) at 37°C 6h.

tag: strain/cell line


title: Prostate_tumour_CPCG0604_rep1

type: genomic

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing:
Raw data were processed through Dasen
The Matrix_processed.txt contains Average Beta
the Matrix_signal_intensities.txt contains unmethylated and methylated signal intensities.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Illumina Infinium HumanMethylation 450k BeadChip kits were used to assess global methylation, using 500 ng of input genomic DNA at the McGill University and Genome Quebec Innovation Centre (Montreal, QC)

value: Sporadic

value: intermediate

value: Fresh frozen


title: Prostate_tumour_CPCG0607_rep1


title: Prostate_tumour_CPCG0600_rep1


title: Prostate_tumour_CPCG0599_rep1


title: Prostate_tumour_CPCG0601_rep1


title: Prostate_tumour_CPCG0609_rep1


title: Prostate_tumour_CPCG0602_rep1


title: Prostate_tumour_CPCG0605_rep1

value: low


title: Prostate_tumour_CPCG0606_rep1


title: RNA-seq_ctrl_kd_rep2


title: Prostate_tumour_CPCG0596_rep1


title: Nucl_Mnase_N-myc_kd_rep1

data_processing:
Basecalls performed using CASAVA version 1.9
MNase-seq reads were cleaned by using trim_galore (v.0.4.4) to remove adapter sequences and low quality sequences.
The clean reads were mapped to the hg19 assembly using bowtie2 (v.2.2.4) with parameters: -I 100 -X 300
The mapped reads were filtered by the following specifications: only the read pairs mapped properly and with a mapq > 10 were retained for further analysis.
The midpoints of proper pairs were used as input to predicted the nucleosome positions by Genetrack.
Genome_build: hg19
Supplementary_files_format_and_content: bed files of predicted nucleosome positions with read count and fuzziness values by Genetrack

extract_protocol:
Lysates  were clarified from nuclei by Mnase.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

treatment_protocol: ~4X105 cells were cultured in dish and incubated with siRNA（siRNA concentration=80nM） and Lipofectamine 2000 (Life Technologies 11668019) in Optimem (Life Technologies 51985034) at 37°C 6h. The next day, isolate the DNA, protein and the cells.

value: N-myc kd


title: RNA-seq_MYCN_kd_rep1

value: MYCN kd


title: RNA-seq_MYCN_kd_rep2


title: Prostate_tumour_CPCG0594_rep1


title: Prostate_tumour_CPCG0598_rep1


title: Prostate_tumour_CPCG0592_rep1


title: Prostate_tumour_CPCG0593_rep1


title: Prostate_tumour_CPCG0595_rep1


title: Prostate_tumour_CPCG0591_rep1


title: Prostate_tumour_CPCG0603_rep1


title: Nucl_Mnase_ctrl_N-myc_kd_rep1


title: Prostate_tumour_CPCG0589_rep1


title: Prostate_tumour_CPCG0590_rep1


title: MCAO3_CD163

tag: strain


title: IgG_MYCN_kd_rep1

data_processing:
Basecalls performed using CASAVA version 1.9
ChIP-seq reads were cleaned by using trim_galore (v.0.4.4) to remove adapter sequences and low quality sequences.
The clean reads were mapped to the hg19 assembly using bowtie2 (v.2.2.4) with parameters: -I 100 -X 500
The mapped reads were filtered by the following specifications: only the read pairs mapped properly and with a mapq≥10 were retained for further analysis.
Bigwig files were generated using Deeptools with parameters: -b 10 --smoothLength 30 --normalizeUsingRPKM
Genome_build: hg19

extract_protocol:
Lysates  were clarified from nuclei by MNase and histone-DNA complexes were isolated with antibody
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

treatment_protocol: ~4X105 cells were cultured in dish and incubated with siRNA（siRNA concentration=80nM） and Lipofectamine 2000 (Life Technologies 11668019) in Optimem (Life Technologies 51985034) at 37°C 6h. The next day, isolate the total DNA and protein and the cells.

tag: chip antibody

value: cell signaling 2729


title: Prostate_tumour_CPCG0588_rep1


title: IgG_ctrl_kd_rep1

tag: genotype


title: Prostate_tumour_CPCG0587_rep1


title: Prostate_tumour_CPCG0582_rep1 [re-analysis]


title: Prostate_tumour_CPCG0580_rep1 [re-analysis]


title: Prostate_tumour_CPCG0581_rep1 [re-analysis]


title: Prostate_tumour_CPCG0579_rep1


title: H3K4me3_MYCN_kd_rep1

value: abcam ab8580


title: H3K9ac_ctrl_kd_rep1

value: abcam ab10812


title: Prostate_tumour_CPCG0584_rep1


title: H3K9ac_MYCN_kd_rep1


title: Prostate_tumour_CPCG0578_rep1 [re-analysis]


title: Prostate_tumour_CPCG0576_rep1 [re-analysis]


title: Prostate_tumour_CPCG0577_rep1 [re-analysis]


title: H3K4me3_ctrl_kd_rep1


title: H3K4me1_MYCN_kd_rep1

value: abcam ab8895


title: Prostate_tumour_CPCG0574_rep1


title: H3K4me1_ctrl_kd_rep1


title: Prostate_tumour_CPCG0575_rep1


title: Prostate_tumour_CPCG0573_rep1


title: Prostate_tumour_CPCG0597_rep1


title: Prostate_tumour_CPCG0572_rep1


title: VOA1056_RNA-Seq

tag: cell type

value: Model of Low Grade Serous Ovarian Cancer


title: Prostate_tumour_CPCG0569_rep1


title: Prostate_tumour_CPCG0567_rep1


title: Prostate_tumour_CPCG0568_rep1


title: H3K27me3_MYCN_kd_rep1

value: active motif 39155


title: Prostate_tumour_CPCG0570_rep1


title: Prostate_tumour_CPCG0571_rep1


title: H3K27me3_ctrl_kd_rep1

value: wild type


title: H3K36me3_ctrl_kd_rep1

value: abcam ab9050


title: Prostate_tumour_CPCG0566_rep1


title: Prostate_tumour_CPCG0563_rep1


title: H3K27ac_ctrl_kd_rep1

value: abcam ab4729


title: Prostate_tumour_CPCG0561_rep1


title: Prostate_tumour_CPCG0562_rep1


title: Prostate_tumour_CPCG0560_rep1


title: H3K27ac_MYCN_kd_rep1


title: Prostate_tumour_CPCG0557_rep1


title: Prostate_tumour_CPCG0559_rep1


title: Prostate_tumour_CPCG0539_rep1


title: Prostate_tumour_CPCG0551_rep1


title: Prostate_tumour_CPCG0545_rep1


title: Prostate_tumour_CPCG0550_rep1


title: Prostate_tumour_CPCG0540_rep1


title: Prostate_tumour_CPCG0547_rep1


title: Prostate_tumour_CPCG0534_rep1


title: Prostate_tumour_CPCG0533_rep1


title: IR5Gy_NPC_RNA-seq

city: Tokyo

first: Mikio

last: Shimada

address: 2-12-1 N1-30 Oookayama, Meouro-ku

department: Institute of Innovative Research

country: Japan

institute: Tokyo Institute of Technology

data_processing:
Basecalls were performed with Hiseq control software 2.2.58 RTA 1.18.64 bclfastq1.8.4.
Raw data was imported to Illumina Basespace Sequence Hub and checked using FASTQ toolkit.
Low-quality (score <20) bases were trimmed from both ends of the reads. Trimmed reads shorter than 40nt or containing many (>20%).
The filter-passed reads were aligned to the human genome hg19 using TopHat2 with --no-novel-juncs option.
The reads mapped in a proper pair were extracted using SAMtools with -f 3 option.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.gene_exp.diff: the comparison of differential expression between Non-IR and IR treated samples in fibroblasts, iPSCs and NPCs.

growth_protocol: Human fibroblasts were cultured with DMEM supplemented with 10% FBS and penicillin and streptmycine, iPS cells derived from human fibroblasts were cultured with Nutristem XF/FF culture medium, neural progenitor cells derived from iPS cells were cultured with neural basal medium.

extract_protocol:
RNA were extracted from IR-treated or non-treated cells using Fast Gene RNA premium kit (Fast Gene). RNA were applied for Illumina Hiseq2500 (Eurofins).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cobalt60 gamma ray irradiation were exposed to the cells.

value: iPS cells-derived neural progenitor cells

tag: passage

value: P1-P3 (after differentiation)

value: IR 5Gy


title: Prostate_tumour_CPCG0532_rep1

value: Sporadic

value: intermediate


title: H3K36me3_MYCN_kd_rep1


title: Prostate_tumour_CPCG0529_rep1

value: Fresh frozen


title: Prostate_tumour_CPCG0531_rep1


title: Prostate_tumour_CPCG0528_rep1


title: Prostate_tumour_CPCG0526_rep1


title: Prostate_tumour_CPCG0527_rep1


title: IR5Gy_iPSC_RNA-seq

source_name: iPS cells

value: fibroblasts-derived iPS cells

value: P2-P5 (after reprogramming)


title: non-IR_NPC_RNA-seq

value: non-IR


title: Prostate_tumour_CPCG0525_rep1


title: Prostate_tumour_CPCG0565_rep1


title: non-IR_iPSC_RNA-seq


title: Prostate_tumour_CPCG0524_rep1


title: Prostate_tumour_CPCG0522_rep1


title: Prostate_tumour_CPCG0523_rep1


title: IR5Gy_Fibroblast_RNA-seq

source_name: Fibroblasts

value: skin fibroblasts


title: Prostate_tumour_CPCG0521_rep1


title: Prostate_tumour_CPCG0520_rep1


title: Prostate_tumour_CPCG0537_rep1


title: siUPF1 of TNRC6A/C

city: Seoul

first: Jin-Wu

last: Nam

address: Seongdong-Gu Hangdang-dong

department: Department of Life Science

country: South Korea

institute: Hanyang University

description: transfected with siRNAs targeting UPF1

data_processing:
RNA-seq data were trimmed by 9 nt for the first fragment of paired-end reads and 6nt for the second of paired-end reads to remove adaptor sequence using seqtk version 1.0. All RNA-seq reads were trimmed with the criterion of the minimum quality 20 and, then, reads with less than 20 nt in length were removed using Sickle version 1.2 (parameters: -q 20 -l 20)
Reads were mapped to the hg19 genomes using Tophat version 2.0.6 (Trapnell et al., 2009), allowing at most five genomic loci mapping, two nucleotide mismatches, and novel introns within one to 99 percentile length of known introns, but not allowing any mismatch at splice sites (parameters: --solexa1.3-quals --splice-mismatches 0 --min-intron-length 61 --max-intron-length 265006 --max-multi hits 5--read-mismatches 2)
Expression level, fragments per kilobase of transcript per million mapped reads (FPKM), were calculated by Cufflinks version 2.1.1 (Trapnell et al., 2010)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: HeLa cell line

growth_protocol: HeLa cells were maintained in DMEM media supplemented with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Cells were seeded one day before transfection with siRNA using Lipofectamine3000 (Invitrogen)

tag: sample type

value: Cell line

value: HeLa

tag: cell origin

value: HeLa cervical cancer cell

value: transfected with siRNAs targeting UPF1


title: siTNRC6A/C

description: transfected with siRNAs targeting TNRC6A/C


title: Prostate_tumour_CPCG0514_rep1

tag: tissue


title: Prostate_tumour_CPCG0508_rep1


title: Prostate_tumour_CPCG0519_rep1


title: Prostate_tumour_CPCG0504_rep1


title: Prostate_tumour_CPCG0507_rep1


title: siTNRC6A/C & siUPF1

description: transfected with siRNAs targeting UPF1 and TNRC6A/C

tag: cell line


title: Prostate_tumour_CPCG0503_rep1

tag: disease state


title: Prostate_tumour_CPCG0509_rep1


title: siControl of SMG7

description: transfected with scrambled siRNAs

value: transfected with scrambled siRNAs


title: Prostate_tumour_CPCG0502_rep1


title: myc-UPF1-WT-siUPF1

description: MYC-tagged UPF1 (wild type) was transfected with siRNAs targeting UPF1


title: siSMG7

description: transfected with siRNAs targeting SMG7

value: transfected with siRNAs targeting SMG7


title: Prostate_tumour_CPCG0498_rep1


title: Prostate_tumour_CPCG0496_rep1


title: Prostate_tumour_CPCG0493_rep1


title: Prostate_tumour_CPCG0499_rep1


title: Prostate_tumour_CPCG0492_rep1


title: Prostate_tumour_CPCG0500_rep1


title: myc-UPF1-MT-siUPF1

description: MYC-tagged UPF1 (helicase mutant, R844C) was transfected with siRNAs targeting UPF1


title: siUPF1 & siDicer1

description: transfected with siRNAs targeting UPF1 and Dicer1


title: non-IR_Fibroblast_RNA-seq


title: siDicer1

description: transfected with siRNAs targeting Dicer1


title: Prostate_tumour_CPCG0486_rep1


title: Prostate_tumour_CPCG0490_rep1


title: Prostate_tumour_CPCG0487_rep1


title: Prostate_tumour_CPCG0489_rep1


title: Prostate_tumour_CPCG0484_rep1


title: siControl of UPF1

description: transfected with scrambled siRNAs


title: Prostate_tumour_CPCG0483_rep1


title: Prostate_tumour_CPCG0482_rep1


title: Prostate_tumour_CPCG0472_rep1


title: siUPF1

description: transfected with siRNAs targeting UPF1


title: Prostate_tumour_CPCG0474_rep1


title: Prostate_tumour_CPCG0470_rep1 [re-analysis]


title: AR-87

city: New York

first: Kemal

middle: Marc

last: Akat

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description:
barcode: TTACA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTACATCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically confirmed acute liver allograft rejection

data_processing:
Base calling was done using CASAVA versions 1.8.2.
The data was processed as described in Brown et al. (2013, Front Genet, 4:145) using a curated miRNA and other non-coding and coding RNA transcriptomes (Akat et. al., PNAS 2014)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: The processed data files contain raw, i.e. not-normalized or transformed, miRNA counts based on unique, individual miRNA sequences, or based on precursor cistrons and sequence families.

source_name: Serum

extract_protocol:
Total RNA was isolated from serum of patients after liver allograft transplantation and used for miRNA-sequencing and qPCR analysis.
The small RNA libraries for the solid tissue samples were prepared using the protocol described in Hafner et al. (Methods, 2008; Methods, 2012) and Akat et al. (PNAS, 2014) with modifications: 1) The libraries were spiked  with 2 cocktails comprising each 10 synthetic 22-nt oligoribonucleotides; the amount of each oligoribonucleotide was 1 amol, 10 amol total for each cocktail, 20 amol total in each sample. 2) The synthetic P32-labeled 19-nt and 24-nt ssRNAs used for size selection were not spiked-into the samples. The sequences for the 20 calibrator oligoribonucleotides are in the supplementary information of this publication.
Directional RNA-seq (size-fractionation for RNAs 19- to 24-nt)

tag: gender

value: female

tag: race

value: white/not hispanic

value: Serum

tag: cause of liver failure

value: Chronic hepatocellular disease:Alcoholic liver disease

tag: library


title: Prostate_tumour_CPCG0468_rep1 [re-analysis]

value: Sporadic


title: AR-85

description:
barcode: TGATG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TGATGTCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically confirmed acute liver allograft rejection

tag: age

value: male

value: Chronic hepatocellular disease:Nonalcoholic steatohepatitis


title: AR-86

description:
barcode: TGTGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TGTGTTCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically confirmed acute liver allograft rejection

value: Glycogen storage disease, type I


title: Prostate_tumour_CPCG0466_rep2 [re-analysis]

value: intermediate

value: Fresh frozen


title: Prostate_tumour_CPCG0466_rep1 [re-analysis]


title: AR-84

description:
barcode: TATCA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TATCATCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically confirmed acute liver allograft rejection


title: Prostate_tumour_CPCG0465_rep1 [re-analysis]


title: Prostate_tumour_CPCG0464_rep1 [re-analysis]


title: Prostate_tumour_CPCG0462_rep1 [re-analysis]


title: Prostate_tumour_CPCG0463_rep1 [re-analysis]


title: AR-57

description:
barcode: TAGAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGAGTCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically confirmed acute liver allograft rejection


title: AR-58

description:
barcode: TAGGA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGGATCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically confirmed acute liver allograft rejection


title: AR-52

description:
barcode: TAATA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAATATCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically confirmed acute liver allograft rejection

value: Cavernous hemangiomas of the liver


title: Prostate_tumour_CPCG0459_rep1 [re-analysis]


title: prostate tumour CPCG0584

description: new

value: prostate tumour

tag: batch


title: Prostate_tumour_CPCG0459_rep2 [re-analysis]


title: Prostate_tumour_CPCG0458_rep1 [re-analysis]


title: AR-50

description:
barcode: TAACG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAACGTCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically confirmed acute liver allograft rejection


title: Prostate_tumour_CPCG0457_rep1 [re-analysis]


title: Prostate_tumour_CPCG0471_rep1 [re-analysis]


title: Prostate_tumour_CPCG0456_rep1 [re-analysis]


title: Prostate_tumour_CPCG0457_rep2 [re-analysis]


title: Prostate_tumour_CPCG0456_rep2 [re-analysis]


title: prostate tumour CPCG0609

description: new


title: AR-44

description:
barcode: TTAAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTAAGTCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically confirmed acute liver allograft rejection


title: Prostate_tumour_CPCG0455_rep2 [re-analysis]


title: prostate tumour CPCG0557

description: new


title: AR-43

description:
barcode: TCGCG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGCGTCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically confirmed acute liver allograft rejection


title: Prostate_tumour_CPCG0454_rep2 [re-analysis]

value: low


title: Prostate_tumour_CPCG0467_rep1 [re-analysis]


title: prostate tumour CPCG0509

description: new


title: Prostate_tumour_CPCG0453_rep2 [re-analysis]


title: AR-46

description:
barcode: TCTAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTAGTCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically confirmed acute liver allograft rejection


title: Prostate_tumour_CPCG0453_rep1 [re-analysis]


title: prostate tumour CPCG0493

description: new


title: Prostate_tumour_CPCG0452_rep3 [re-analysis]


title: AR-41

description:
barcode: TCGAT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGATTCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically confirmed acute liver allograft rejection

value: Chronic hepatocellular disease:Antitrypsin deficiency


title: prostate tumour CPCG0607

description: new


title: AR-33

description:
barcode: TCTGA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTGATCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically confirmed acute liver allograft rejection


title: Prostate_tumour_CPCG0452_rep2 [re-analysis]


title: AR-30

description:
barcode: TCCTA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCTATCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically confirmed acute liver allograft rejection

value: black


title: Prostate_tumour_CPCG0451_rep2 [re-analysis]


title: Prostate_tumour_CPCG0452_rep1 [re-analysis]


title: N-92

description:
barcode: TCTCC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTCCTCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically normal liver biopsy.


title: prostate tumour CPCG0605

description: new


title: Prostate_tumour_CPCG0455_rep1 [re-analysis]


title: prostate tumour CPCG0604

description: new


title: N-65

description:
barcode: TCTAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTAGTCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically normal liver biopsy.


title: N-64

description:
barcode: TCGCG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGCGTCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically normal liver biopsy.


title: Prostate_tumour_CPCG0439_rep2 [re-analysis]


title: Prostate_tumour_CPCG0448_rep1 [re-analysis]


title: Prostate_tumour_CPCG0451_rep1 [re-analysis]


title: Prostate_tumour_CPCG0448_rep3 [re-analysis]


title: Prostate_tumour_CPCG0448_rep2 [re-analysis]


title: Prostate_tumour_CPCG0445_rep1 [re-analysis]


title: Prostate_tumour_CPCG0454_rep1 [re-analysis]


title: prostate tumour CPCG0603

description: new


title: N-56

description:
barcode: TCCGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCGTTCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically normal liver biopsy.

value: Chronic hepatocellular disease:Cryptogenic cirrhosis


title: Prostate_tumour_CPCG0437_rep1


title: N-55

description:
barcode: TCCAC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCACTCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically normal liver biopsy.


title: prostate tumour CPCG0602

description: new


title: Prostate_tumour_CPCG0439_rep1 [re-analysis]


title: Prostate_tumour_CPCG0435_rep2 [re-analysis]


title: prostate tumour CPCG0606

description: new


title: N-54

description:
barcode: TCATC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCATCTCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically normal liver biopsy.

value: Hepatocellular carcinoma, stage II


title: prostate tumour CPCG0600

description: new


title: Prostate_tumour_CPCG0433_rep1


title: Prostate_tumour_CPCG0434_rep1 [re-analysis]


title: Prostate_tumour_CPCG0432_rep1


title: prostate tumour CPCG0599

description: new


title: N-53

description:
barcode: TCACT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCACTTCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically normal liver biopsy.


title: N-51

description:
barcode: TGTGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TGTGTTCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically normal liver biopsy.


title: Prostate_tumour_CPCG0428_rep1 [re-analysis]


title: prostate tumour CPCG0598

description: new


title: Prostate_tumour_CPCG0426_rep2


title: Prostate_tumour_CPCG0426_rep1


title: Prostate_tumour_CPCG0424_rep2


title: N-49

description:
barcode: TGATG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TGATGTCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically normal liver biopsy.

value: female


title: prostate tumour CPCG0597

description: new


title: N-48

description:
barcode: TATCA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TATCATCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically normal liver biopsy.

value: white/not hispanic


title: Prostate_tumour_CPCG0424_rep1


title: prostate tumour CPCG0596

description: new


title: Prostate_tumour_CPCG0423_rep3


title: Prostate_tumour_CPCG0435_rep1 [re-analysis]


title: prostate tumour CPCG0595

description: new


title: Prostate_tumour_CPCG0418_rep1 [re-analysis]


title: Prostate_tumour_CPCG0418_rep2 [re-analysis]


title: Prostate_tumour_CPCG0423_rep1 [re-analysis]


title: prostate tumour CPCG0601

description: new


title: prostate tumour CPCG0594

description: new


title: N-31

value: Serum


title: Prostate_tumour_CPCG0434_rep2 [re-analysis]


title: N-45

value: Chronic hepatocellular disease:Alcoholic liver disease


title: Prostate_tumour_CPCG0416_rep1 [re-analysis]

value: Sporadic


title: Prostate_tumour_CPCG0415_rep1 [re-analysis]


title: N-37

value: male


title: N-27

description:
barcode: TAGGA
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGGATCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically normal liver biopsy.


title: Prostate_tumour_CPCG0423_rep4


title: prostate tumour CPCG0593

description: new


title: prostate tumour CPCG0592

description: new


title: prostate tumour CPCG0591

description: new


title: N-20

description:
barcode: TAGAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TAGAGTCGTATGCCGTCTTCTGCTTG
Serum from patient with histologically normal liver biopsy.


title: prostate tumour CPCG0590

description: new


title: Prostate_tumour_CPCG0413_rep1 [re-analysis]


title: Prostate_tumour_CPCG0423_rep2 [re-analysis]


title: prostate tumour CPCG0589

description: new


title: N-18


title: Prostate_tumour_CPCG0410_rep1 [re-analysis]


title: Prostate_tumour_CPCG0407_rep1 [re-analysis]


title: Prostate_tumour_CPCG0411_rep1 [re-analysis]


title: Prostate_tumour_CPCG0408_rep1 [re-analysis]

value: high


title: prostate tumour CPCG0587

description: new


title: prostate tumour CPCG0588

description: new


title: Prostate_tumour_CPCG0409_rep1 [re-analysis]


title: Prostate_tumour_CPCG0411_rep2 [re-analysis]


title: prostate tumour CPCG0582

description: new


title: Prostate_tumour_CPCG0406_rep2 [re-analysis]


title: Prostate_tumour_CPCG0404_rep2 [re-analysis]


title: Prostate_tumour_CPCG0414_rep1 [re-analysis]


title: Prostate_tumour_CPCG0401_rep1 [re-analysis]


title: Prostate_tumour_CPCG0402_rep1 [re-analysis]


title: Prostate_tumour_CPCG0404_rep1 [re-analysis]


title: Prostate_tumour_CPCG0412_rep1 [re-analysis]


title: Prostate_tumour_CPCG0398_rep3 [re-analysis]


title: prostate tumour CPCG0580

description: new


title: Prostate_tumour_CPCG0397_rep1 [re-analysis]


title: Prostate_tumour_CPCG0398_rep1 [re-analysis]


title: Prostate_tumour_CPCG0397_rep2 [re-analysis]


title: Prostate_tumour_CPCG0396_rep4 [re-analysis]


title: Prostate_tumour_CPCG0396_rep2 [re-analysis]


title: Prostate_tumour_CPCG0396_rep3 [re-analysis]


title: Prostate_tumour_CPCG0406_rep1 [re-analysis]


title: prostate tumour CPCG0578

description: new


title: Prostate_tumour_CPCG0395_rep2 [re-analysis]


title: Prostate_tumour_CPCG0395_rep1 [re-analysis]


title: Prostate_tumour_CPCG0392_rep2 [re-analysis]


title: prostate tumour CPCG0581

description: new


title: prostate tumour CPCG0575

description: new


title: Prostate_tumour_CPCG0392_rep3 [re-analysis]


title: prostate tumour CPCG0574

description: new


title: Prostate_tumour_CPCG0398_rep2 [re-analysis]


title: prostate tumour CPCG0573

description: new


title: Prostate_tumour_CPCG0392_rep1 [re-analysis]


title: Prostate_tumour_CPCG0388_rep3 [re-analysis]


title: prostate tumour CPCG0579

description: new


title: Prostate_tumour_CPCG0391_rep1 [re-analysis]


title: Prostate_tumour_CPCG0391_rep2 [re-analysis]


title: Prostate_tumour_CPCG0388_rep2 [re-analysis]


title: prostate tumour CPCG0572

description: new


title: prostate tumour CPCG0577

description: new


title: Prostate_tumour_CPCG0387_rep1 [re-analysis]


title: prostate tumour CPCG0576

description: new


title: Prostate_tumour_CPCG0396_rep1 [re-analysis]


title: prostate tumour CPCG0570

description: new


title: Prostate_tumour_CPCG0382_rep2 [re-analysis]


title: Prostate_tumour_CPCG0382_rep1 [re-analysis]


title: prostate tumour CPCG0569

description: new


title: prostate tumour CPCG0568

description: new


title: melanocytes senescence 3

city: Linköping

first: Karin

last: Öllinger

address: Medicinska fakulteten

department: Experimental Pathology, Department of Clinical and Experimental Medicine

country: Sweden

institute: Linköping University

description: senescent melanocytes

hyb_protocol: Hybridisation was performed with the Affymetrix Human Genome Microarray (WT GeneTitan ST1.1; Plate type, HuGene-1_1-st-v1-16; Array type, HuGene-1_1-st-v1) according to the manufacturer’s protocols (Affymetrix Inc., CA, USA)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Scanned images (DAT files) were transformed into intensities (CEL files) by GCOS (Affymetrix). The data were processed using the Agilent GeneSpring GX 13 software package (Agilent Technologies, Santa Clara, CA, USA). The exon-level data were summarized using the RMA16 algorithm and the baseline was transformed to the median of all samples. The exon-level analysis includes multiple probe sets that correspond to the same gene.  Entities are filtered, based on their signal intensity values, between 20 and 100 percentile in at least 1 sample. For the gene-level experiment the data were normalized with a quantile algorithm and the baseline was transformed to the median of all samples. The gene-level analysis summarizes all probe sets corresponding to the same gene.  The Gene_ID column lists all probe sets that were summarized for each gene.

source_name: senescent melanocytes

label_protocol: Labelling was performed with the Affymetrix Human Genome Microarray (WT GeneTitan ST1.1; Plate type, HuGene-1_1-st-v1-16; Array type, HuGene-1_1-st-v1) according to the manufacturer’s protocols (Affymetrix Inc., CA, USA)

growth_protocol: Melanocytes were obtained from Caucasian donors (0-3 years of age) by means of foreskin circumcisions. The melanocytes were cultured in Medium 199 with supplements and incubated at 37°C in a humidified atmosphere of 5% CO2 in air. The first sample (young) was taken 3 days after isolation/seeding and the second sample (senescent) was isolated after a minimum of 30 days when the cells showed senescent-like morphology, i.e. flattened and non-proliferative.

extract_protocol: After isolation of total RNA (TRIzol, Sigma), the quality was controlled using an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

value: foreskin

value: melanocytes

tag: cell phenotype

value: senescent


title: prostate tumour CPCG0567

description: new

value: intermediate


title: Prostate_tumour_CPCG0379_rep1 [re-analysis]

value: Fresh frozen


title: Prostate_tumour_CPCG0380_rep1 [re-analysis]


title: melanocytes senescence 2

description: senescent melanocytes


title: Prostate_tumour_CPCG0381_rep1 [re-analysis]


title: Prostate_tumour_CPCG0377_rep1 [re-analysis]


title: Prostate_tumour_CPCG0375_rep2 [re-analysis]

value: low


title: prostate tumour CPCG0571

description: new

value: prostate tumour


title: prostate tumour CPCG0566

description: new


title: Prostate_tumour_CPCG0388_rep1 [re-analysis]


title: melanocytes senescence 4

description: senescent melanocytes


title: Prostate_tumour_CPCG0375_rep1 [re-analysis]


title: Anolis forelimb D5 rep3

city: West Haven

first: Cong

last: Liang

address: 300 Heffernan Dr.

institute: Yale University

description:
Ac_FL_D5_Rep3
processed data file:
ac_HTSeq_upload.txt

data_processing:
Basecalls performed using CASAVA
mRNA-seq reads were aligned to the alligator (allMis0.2), Anolis (AnoCar2.0), and mouse (GRCm38) cDNA builds using Tophat2
Number of reads overlapped with known features (gene counts) was counted using HTSeq
transcripts per million (TPM) values were calculated according to Wagner et al (2012) Theor. Biosci.
Genome_build: alligator (allMis0.2), Anolis (AnoCar2.0), and mouse (GRCm38)
Supplementary_files_format_and_content: tab-delimited txt files include read counts for each sample.  Gene IDs for Anolis and Mouse are from Ensembl while alligator gene IDs are available at: http://crocgenome.hpc.msstate.edu

organism: Anolis carolinensis

source_name: forelimb digit5

extract_protocol:
Tissues were harvested and kept in RNAlater until extraction of RNA using Qiagen RNeasy extraction kit.
RNA libraries for alligator and mouse were prepared for sequencing using standard illumina protocols. Anolis RNA libraries were prepared using Clontech's Ultra Low V4 kit (Catalog # 634890).

tag: developmental stage

value: stage 10

value: forelimb digit5


title: Anolis forelimb D5 rep2

description:
Ac_FL_D5_Rep2
processed data file:
ac_HTSeq_upload.txt


title: melanocytes senescence 1

description: senescent melanocytes


title: prostate tumour CPCG0565

description: new


title: melanocytes normal 3

description: young melanocytes

source_name: young melanocytes

value: young


title: Prostate_tumour_CPCG0374_rep2 [re-analysis]


title: Prostate_tumour_CPCG0381_rep2 [re-analysis]


title: melanocytes normal 4

description: young melanocytes


title: melanocytes normal 2

description: young melanocytes


title: Anolis forelimb D5 rep1

description:
Ac_FL_D5_Rep1
processed data file:
ac_HTSeq_upload.txt


title: Prostate_tumour_CPCG0379_rep2 [re-analysis]


title: melanocytes normal 1

description: young melanocytes


title: prostate tumour CPCG0563

description: new


title: Prostate_tumour_CPCG0374_rep1 [re-analysis]


title: Prostate_tumour_CPCG0373_rep1 [re-analysis]


title: Prostate_tumour_CPCG0378_rep1 [re-analysis]


title: Prostate_tumour_CPCG0372_rep1 [re-analysis]


title: prostate tumour CPCG0562

description: new


title: Anolis forelimb D4 rep3

description:
Ac_FL_D4_Rep3
processed data file:
ac_HTSeq_upload.txt

source_name: forelimb digit4

value: forelimb digit4


title: prostate tumour CPCG0561

description: new


title: Anolis forelimb D4 rep2

description:
Ac_FL_D4_Rep2
processed data file:
ac_HTSeq_upload.txt


title: Prostate_tumour_CPCG0368_rep2 [re-analysis]


title: Prostate_tumour_CPCG0371_rep1 [re-analysis]


title: prostate tumour CPCG0560

description: new


title: Anolis forelimb D4 rep1

description:
Ac_FL_D4_Rep1
processed data file:
ac_HTSeq_upload.txt


title: Prostate_tumour_CPCG0366_rep3 [re-analysis]


title: Prostate_tumour_CPCG0366_rep2 [re-analysis]


title: prostate tumour CPCG0559

description: new


title: Prostate_tumour_CPCG0366_rep1 [re-analysis]


title: Anolis forelimb D3 rep3

description:
Ac_FL_D3_Rep3
processed data file:
ac_HTSeq_upload.txt

source_name: forelimb digit3

value: forelimb digit3


title: Prostate_tumour_CPCG0365_rep4 [re-analysis]


title: prostate tumour CPCG0550

description: new


title: prostate tumour CPCG0551

description: new


title: Anolis forelimb D3 rep1

description:
Ac_FL_D3_Rep1
processed data file:
ac_HTSeq_upload.txt


title: Prostate_tumour_CPCG0364_rep2 [re-analysis]


title: Prostate_tumour_CPCG0364_rep1 [re-analysis]


title: Prostate_tumour_CPCG0363_rep1 [re-analysis]


title: Prostate_tumour_CPCG0365_rep1 [re-analysis]


title: Prostate_tumour_CPCG0365_rep2 [re-analysis]


title: Prostate_tumour_CPCG0365_rep3 [re-analysis]


title: Anolis forelimb D3 rep2

description:
Ac_FL_D3_Rep2
processed data file:
ac_HTSeq_upload.txt


title: prostate tumour CPCG0547

description: new


title: Prostate_tumour_CPCG0368_rep1 [re-analysis]


title: Prostate_tumour_CPCG0362_rep2 [re-analysis]


title: Anolis forelimb D2 rep3

description:
Ac_FL_D2_Rep3
processed data file:
ac_HTSeq_upload.txt

source_name: forelimb digit2

value: forelimb digit2


title: Anolis forelimb D2 rep1

description:
Ac_FL_D2_Rep1
processed data file:
ac_HTSeq_upload.txt


title: prostate tumour CPCG0545

description: new


title: Prostate_tumour_CPCG0362_rep1 [re-analysis]


title: Prostate_tumour_CPCG0361_rep1 [re-analysis]


title: prostate tumour CPCG0539

description: new


title: Prostate_tumour_CPCG0361_rep2 [re-analysis]


title: Anolis forelimb D2 rep2

description:
Ac_FL_D2_Rep2
processed data file:
ac_HTSeq_upload.txt


title: prostate tumour CPCG0540

description: new


title: Prostate_tumour_CPCG0369_rep1 [re-analysis]


title: Anolis forelimb D1 rep3

description:
Ac_FL_D1_Rep3
processed data file:
ac_HTSeq_upload.txt

source_name: forelimb digit1

value: forelimb digit1


title: Prostate_tumour_CPCG0360_rep2 [re-analysis]

value: Sporadic


title: Prostate_tumour_CPCG0360_rep1 [re-analysis]


title: Anolis forelimb D1 rep2

description:
Ac_FL_D1_Rep2
processed data file:
ac_HTSeq_upload.txt


title: Prostate_tumour_CPCG0358_rep1 [re-analysis]


title: prostate tumour CPCG0537

description: new


title: Prostate_tumour_CPCG0357_rep2 [re-analysis]


title: Prostate_tumour_CPCG0357_rep1 [re-analysis]


title: prostate tumour CPCG0534

description: new


title: prostate tumour CPCG0533

description: new


title: Prostate_tumour_CPCG0356_rep1 [re-analysis]


title: Prostate_tumour_CPCG0355_rep1 [re-analysis]


title: Prostate_tumour_CPCG0354_rep1 [re-analysis]


title: VP_scRNA_seq2_cell_96 dataset #3

city: Montréal

first: Claire

middle: Elizabeth

last: Nash

state: QC

address: 1001 Decarie Blvd

department: Urology

institute: Research Institute of McGill University Health Centre

description:
Rat_scRNAseq_Expr_Counts_VP2.txt
single-cell RNA sequencing Fluidigm C1

data_processing:
ChIP-seq reads were aligned to the rnor6.0 genome assembly using Bowtie2 with default parameters
Duplicate ChIP-seq reads were removed using MarkDuplicates and uniquely mapped reads were determined using MAPQ score>=25 with Samtools
ChIP-seq peaks were called using MACS 2.0.10 cutoff of p-value = 1e-7
ChIP-seq peaks were called using HOMER with default settings
ChIP-seq shared peaks (called by both algorithms) were determined using HOMER mergePeaks
RNA-seq reads were aligned to the Ensembl Rnor6.0 genome assembly using Tophat 2.1.0
ChIP-seq and RNA-seq uniquely mapped reads were determined using MAPQ score>=25 with Samtools
RNA-seq read counts were quantified with featureCounts and TPM calculated
Single-cell RNA-seq raw paired-end reads were trimmed using Trimmomatic v0.33, to a minimum length of 30 nucleotides. Illumina Nextera XT adapters were removed in palindrome mode. A minimum Phred quality score of 30 was required for the 3’end. Single end reads as well as paired end reads failing previous minimum quality controls were discarded. Individual read groups were aligned, using TopHat first against the rat transcriptome as defined by the Ensembl gene models version 83, with default parameters and the remaining unmapped genes to the Ensembl Rnor_6.0 reference rat genome from Illumina iGenomes web site.  Trimming rates and insert length were controlled on each read group based on metrics reported by Trimmomatic, and Picard v1.128 respectively. Aligned reads from multiple read groups belonging to the same sample were indexed, sorted and merged using sambamba v0.5.1, a faster implementation of the Samtools algorithms. Amplification duplicates were removed using Picard v1.128. Various quality controls from the RNA-SeQC package were used, including the genes detected, mapping rates, duplication rates, and intronic rate, based on metrics collected for each sample used.
Single-cell RNA-seq read counts were quantified using HTSeq Count using Ensembl Rnor_6.0 and TPM calculated
Genome_build: Ensembl Rnor_6.0
Supplementary_files_format_and_content: bigwig files were generated by converting bedgraph to bigwig files using the bedGraphToBigWig UCSC converter. Scores represent treatment pileup
Supplementary_files_format_and_content: Shared peak files were determined using HOMER mergePeaks and then annoated relative to genes using HOMER AnnotatePeaks.
Supplementary_files_format_and_content: RNA-seq read counts were quantified with featureCounts and TPM calculated
Supplementary_files_format_and_content: Single-cell RNA-seq read counts were quantified using HTSeq Count using Ensembl Rnor_6.0 and TPM calculated

source_name: Male urogenital sinus

extract_protocol:
Tissues were disscociated with 2mg/mL Collagenase 1A (Sigma-Aldrich, Missouri, USA) for 60 minutes at 37 degrees C. Dispersed fibroblasts were separated by centrifugation and passing through a 0.7um cell strainer (Falcon, Corning, New York, USA). Cell suspensions were centrifuged for 10 minutes at 500g and resuspended in LIVE/DEAD Cell Viability/Cytotoxicity Assay for mammalian cells (ThermoFisher, L-3224).   After a 10 minute incubation at room temperature, cells were centrifuged and resuspended in Cell Wash Buffer (Fluidigm).  Cell concentration, size and viability were verified on hemocytometers (Incyto DHC-N01-5) through bright field, GFP and RFP on a EVOS FL Auto microscope (ThermoFisher).  Single cell RNA libraries were constructed according to the Fluidigm protocol using C1 to generate libraries for RNA sequencing (PN 100-7168).
Single cell RNA libraries were constructed according to the Fluidigm protocol using C1 to generate libraries for RNA sequencing (PN 100-7168).  Briefly, full length mRNA-Seq libraries were generated from single-cells captured on the Fluidigm C1 platform using SMARTer Ultra Low RNA Kit (P/N 634936 Clontech). ERCC RNA Spike-In mix (P/N 4456740 ThermoFisher) was added to the lysis mix for normalization and quality control purposes. Full length cDNAs were converted into sequence ready libraries using Nextera XT DNA Sample Preparation Kit (P/N FC-131-1096 Illumina), and sequenced on an Illumina HiSeq 2000 with paired-end 100bp read option. The Fluidigm C1 platform captured 52 and 70 single cells from VMP and SU respectively. The average full length cDNA yield/min/max were 6.06ng(+/-0.12)/2.25ng/14.81ng for VMP and 8.51ng(+/-0.21)/2.55ng/26.6ng for SU.  Libraries from 52 VMP and 63 SU single cells were sequenced.
Lysates were clarified from sonicated nuclei and AR-DNA complexes were isolated with antibody.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end)

tag: tissue subset

value: Ventral prostate (VP)

value: P0 (day of birth)

tag: strain

value: Wistar


title: Prostate_tumour_CPCG0353_rep2 [re-analysis]


title: prostate tumour CPCG0532

description: new

source_name: Fresh frozen prostate tumour


title: prostate tumour CPCG0531

description: new


title: Prostate_tumour_CPCG0353_rep1 [re-analysis]


title: VP_scRNA_seq2_cell_95 dataset #3


title: Prostate_tumour_CPCG0352_rep1 [re-analysis]


title: VP_scRNA_seq2_cell_93 dataset #3


title: prostate tumour CPCG0528

description: new


title: Prostate_tumour_CPCG0348_rep1 [re-analysis]


title: prostate tumour CPCG0529

description: new


title: Prostate_tumour_CPCG0349_rep1 [re-analysis]


title: VP_scRNA_seq2_cell_90 dataset #3


title: Prostate_tumour_CPCG0350_rep1 [re-analysis]

value: high


title: Prostate_tumour_CPCG0346_rep3 [re-analysis]


title: Prostate_tumour_CPCG0346_rep1 [re-analysis]


title: prostate tumour CPCG0527

description: new


title: VP_scRNA_seq2_cell_89 dataset #3


title: Prostate_tumour_CPCG0345_rep4 [re-analysis]


title: Prostate_tumour_CPCG0346_rep2 [re-analysis]


title: Prostate_tumour_CPCG0345_rep3 [re-analysis]


title: VP_scRNA_seq2_cell_88 dataset #3


title: Anolis forelimb D1 rep1

description:
Ac_FL_D1_Rep1
processed data file:
ac_HTSeq_upload.txt


title: Prostate_tumour_CPCG0345_rep2 [re-analysis]


title: prostate tumour CPCG0526

description: new


title: VP_scRNA_seq2_cell_86 dataset #3


title: prostate tumour CPCG0525

description: new


title: Prostate_tumour_CPCG0345_rep1 [re-analysis]


title: VP_scRNA_seq2_cell_85 dataset #3


title: Prostate_tumour_CPCG0344_rep2 [re-analysis]


title: Prostate_tumour_CPCG0344_rep1 [re-analysis]


title: Prostate_tumour_CPCG0341_rep2 [re-analysis]


title: VP_scRNA_seq2_cell_84 dataset #3


title: prostate tumour CPCG0524

description: new


title: prostate tumour CPCG0508

description: new


title: VP_scRNA_seq2_cell_92 dataset #3


title: Prostate_tumour_CPCG0341_rep1 [re-analysis]


title: prostate tumour CPCG0504

description: new


title: VP_scRNA_seq2_cell_83 dataset #3


title: prostate tumour CPCG0503

description: new


title: prostate tumour CPCG0502

description: new


title: Prostate_tumour_CPCG0336_rep2 [re-analysis]


title: Prostate_tumour_CPCG0340_rep2 [re-analysis]


title: Prostate_tumour_CPCG0339_rep1 [re-analysis]


title: prostate tumour CPCG0500

description: new


title: Prostate_tumour_CPCG0340_rep1 [re-analysis]


title: Prostate_tumour_CPCG0335_rep1 [re-analysis]


title: Prostate_tumour_CPCG0336_rep1 [re-analysis]


title: VP_scRNA_seq2_cell_81 dataset #3


title: Prostate_tumour_CPCG0334_rep3 [re-analysis]


title: Prostate_tumour_CPCG0335_rep2 [re-analysis]


title: VP_scRNA_seq2_cell_77 dataset #3


title: Prostate_tumour_CPCG0334_rep2 [re-analysis]


title: prostate tumour CPCG0499

description: new


title: Prostate_tumour_CPCG0342_rep1 [re-analysis]


title: Prostate_tumour_CPCG0333_rep2 [re-analysis]


title: prostate tumour CPCG0498

description: new


title: Prostate_tumour_CPCG0333_rep1 [re-analysis]


title: VP_scRNA_seq2_cell_76 dataset #3


title: VP_scRNA_seq2_cell_75 dataset #3


title: Prostate_tumour_CPCG0328_rep1 [re-analysis]


title: Prostate_tumour_CPCG0331_rep1 [re-analysis]


title: VP_scRNA_seq2_cell_72 dataset #3


title: Prostate_tumour_CPCG0324_rep2 [re-analysis]


title: prostate tumour CPCG0490

description: new


title: prostate tumour CPCG0492

description: new


title: Prostate_tumour_CPCG0322_rep1 [re-analysis]


title: VP_scRNA_seq2_cell_80 dataset #3


title: prostate tumour CPCG0496

description: new


title: VP_scRNA_seq2_cell_71 dataset #3


title: VP_scRNA_seq2_cell_70 dataset #3


title: prostate tumour CPCG0486

description: new


title: Prostate_tumour_CPCG0321_rep1 [re-analysis]


title: prostate tumour CPCG0437

description: new


title: Prostate_tumour_CPCG0320_rep1 [re-analysis]


title: Prostate_tumour_CPCG0317_rep2 [re-analysis]


title: Prostate_tumour_CPCG0317_rep1 [re-analysis]


title: prostate tumour CPCG0433

description: new


title: Prostate_tumour_CPCG0315_rep2 [re-analysis]


title: VP_scRNA_seq2_cell_68 dataset #3


title: Prostate_tumour_CPCG0324_rep1 [re-analysis]


title: VP_scRNA_seq2_cell_66 dataset #3


title: Prostate_tumour_CPCG0315_rep1 [re-analysis]


title: prostate tumour CPCG0432

description: new


title: Prostate_tumour_CPCG0314_rep1 [re-analysis]


title: Prostate_tumour_CPCG0313_rep1 [re-analysis]


title: VP_scRNA_seq2_cell_65 dataset #3


title: Prostate_tumour_CPCG0323_rep1 [re-analysis]


title: prostate tumour CPCG0426

description: new


title: Prostate_tumour_CPCG0312_rep1 [re-analysis]


title: Prostate_tumour_CPCG0310_rep2 [re-analysis]


title: Prostate_tumour_CPCG0310_rep1 [re-analysis]


title: VP_scRNA_seq2_cell_61 dataset #3


title: VP_scRNA_seq2_cell_64 dataset #3


title: prostate tumour CPCG0192

description: new


title: Prostate_tumour_CPCG0307_rep1 [re-analysis]


title: Prostate_tumour_CPCG0306_rep2 [re-analysis]


title: VP_scRNA_seq2_cell_60 dataset #3


title: prostate tumour CPCG0507

description: new


title: Prostate_tumour_CPCG0306_rep1 [re-analysis]


title: Prostate_tumour_CPCG0304_rep2 [re-analysis]


title: VP_scRNA_seq2_cell_57 dataset #3


title: VP_scRNA_seq2_cell_58 dataset #3


title: prostate tumour CPCG0523

description: new


title: Prostate_tumour_CPCG0302_rep2 [re-analysis]


title: Prostate_tumour_CPCG0304_rep1 [re-analysis]


title: Prostate_tumour_CPCG0302_rep1 [re-analysis]


title: VP_scRNA_seq2_cell_56 dataset #3


title: prostate tumour CPCG0522

description: new


title: Prostate_tumour_CPCG0301_rep2 [re-analysis]


title: Prostate_tumour_CPCG0312_rep2 [re-analysis]


title: VP_scRNA_seq2_cell_82 dataset #3


title: Prostate_tumour_CPCG0301_rep1 [re-analysis]


title: prostate tumour CPCG0424

description: new


title: Prostate_tumour_CPCG0300_rep2 [re-analysis]


title: prostate tumour CPCG0521

description: new


title: Prostate_tumour_CPCG0300_rep1 [re-analysis]


title: VP_scRNA_seq2_cell_54 dataset #3


title: Prostate_tumour_CPCG0299_rep2 [re-analysis]


title: prostate tumour CPCG0520

description: new


title: prostate tumour CPCG0519

description: new


title: prostate tumour CPCG0514

description: new


title: Prostate_tumour_CPCG0298_rep1 [re-analysis]


title: Prostate_tumour_CPCG0299_rep1 [re-analysis]


title: VP_scRNA_seq2_cell_51 dataset #3


title: Prostate_tumour_CPCG0297_rep1 [re-analysis]


title: VP_scRNA_seq2_cell_53 dataset #3


title: prostate tumour CPCG0489

description: new


title: VP_scRNA_seq2_cell_22 dataset #3


title: prostate tumour CPCG0487

description: new


title: VP_scRNA_seq2_cell_13 dataset #3


title: prostate tumour CPCG0484

description: new


title: VP_scRNA_seq2_cell_50 dataset #3


title: Prostate_tumour_CPCG0296_rep1 [re-analysis]


title: Prostate_tumour_CPCG0291_rep1 [re-analysis]


title: Prostate_tumour_CPCG0293_rep1 [re-analysis]


title: prostate tumour CPCG0483

description: new


title: Prostate_tumour_CPCG0295_rep1 [re-analysis]


title: Prostate_tumour_CPCG0292_rep1 [re-analysis]


title: Prostate_tumour_CPCG0290_rep2 [re-analysis]


title: Prostate_tumour_CPCG0298_rep2 [re-analysis]


title: Prostate_tumour_CPCG0288_rep2 [re-analysis]


title: Prostate_tumour_CPCG0289_rep1 [re-analysis]


title: VP_scRNA_seq2_cell_11 dataset #3


title: VP_scRNA_seq2_cell_04 dataset #3


title: VP_scRNA_seq2_cell_69 dataset #3


title: prostate tumour CPCG0474

description: new


title: Prostate_tumour_CPCG0290_rep1 [re-analysis]


title: prostate tumour CPCG0482

description: new


title: Prostate_tumour_CPCG0287_rep1 [re-analysis]


title: Prostate_tumour_CPCG0286_rep1 [re-analysis]


title: Prostate_tumour_CPCG0288_rep1 [re-analysis]


title: prostate tumour CPCG0472

description: new


title: Prostate_tumour_CPCG0296_rep2 [re-analysis]


title: VP_scRNA_seq2_cell_03 dataset #3


title: Prostate_tumour_CPCG0285_rep1 [re-analysis]


title: prostate tumour CPCG0471

description: new


title: Prostate_tumour_CPCG0282_rep2 [re-analysis]


title: Prostate_tumour_CPCG0282_rep3 [re-analysis]


title: VP_scRNA_seq2_cell_74 dataset #3


title: Prostate_tumour_CPCG0282_rep1 [re-analysis]


title: prostate tumour CPCG0470

description: new


title: VP_scRNA_seq2_cell_06 dataset #3


title: Prostate_tumour_CPCG0279_rep1 [re-analysis]


title: prostate tumour CPCG0468

description: new


title: VP_scRNA_seq2_cell_26 dataset #3


title: prostate tumour CPCG0467

description: new


title: VP_scRNA_seq2_cell_21 dataset #3


title: Prostate_tumour_CPCG0271_rep1 [re-analysis]


title: VP_scRNA_seq2_cell_19 dataset #3


title: Prostate_tumour_CPCG0269_rep1 [re-analysis]


title: Prostate_tumour_CPCG0334_rep1 [re-analysis]


title: Prostate_tumour_CPCG0271_rep2 [re-analysis]


title: prostate tumour CPCG0466

description: new


title: prostate tumour CPCG0465

description: new


title: VP_scRNA_seq2_cell_12 dataset #3


title: Prostate_tumour_CPCG0267_rep2 [re-analysis]


title: Prostate_tumour_CPCG0266_rep2 [re-analysis]


title: Prostate_tumour_CPCG0266_rep1 [re-analysis]


title: Prostate_tumour_CPCG0267_rep1 [re-analysis]


title: prostate tumour CPCG0464

description: new


title: VP_scRNA_seq2_cell_01 dataset #3


title: Prostate_tumour_CPCG0265_rep2 [re-analysis]


title: VP_scRNA_seq2_cell_08 dataset #3


title: prostate tumour CPCG0463

description: new


title: Prostate_tumour_CPCG0265_rep1 [re-analysis]


title: Prostate_tumour_CPCG0281_rep1 [re-analysis]


title: prostate tumour CPCG0462

description: new


title: Prostate_tumour_CPCG0262_rep1 [re-analysis]


title: Prostate_tumour_CPCG0268_rep1 [re-analysis]


title: prostate tumour CPCG0458

description: new


title: Prostate_tumour_CPCG0260_rep1 [re-analysis]


title: Prostate_tumour_CPCG0258_rep2 [re-analysis]


title: Prostate_tumour_CPCG0259_rep1 [re-analysis]


title: Prostate_tumour_CPCG0258_rep1 [re-analysis]


title: Prostate_tumour_CPCG0256_rep3 [re-analysis]


title: VMP_scRNA_seq2_cell_94 dataset #3

description:
Rat_scRNAseq_Expr_Counts_VMP2.txt
single-cell RNA sequencing Fluidigm C1

source_name: Female urogenital sinus

value: Ventral mesenchymal pad (VMP)


title: prostate tumour CPCG0457

description: new

value: intermediate


title: VMP_scRNA_seq2_cell_95 dataset #3


title: VP_scRNA_seq2_cell_10 dataset #3


title: Prostate_tumour_CPCG0256_rep1 [re-analysis]

value: Fresh frozen


title: prostate tumour CPCG0456

description: new


title: Prostate_tumour_CPCG0251_rep1 [re-analysis]


title: Prostate_tumour_CPCG0263_rep1 [re-analysis]


title: VP_scRNA_seq2_cell_09 dataset #3


title: Prostate_tumour_CPCG0249_rep1 [re-analysis]


title: prostate tumour CPCG0454

description: new

value: low


title: Prostate_tumour_CPCG0255_rep2 [re-analysis]


title: Prostate_tumour_CPCG0250_rep1 [re-analysis]


title: VMP_scRNA_seq2_cell_93 dataset #3


title: Prostate_tumour_CPCG0248_rep1 [re-analysis]


title: prostate tumour CPCG0459

description: new

value: prostate tumour


title: Prostate_tumour_CPCG0256_rep2 [re-analysis]


title: VMP_scRNA_seq2_cell_88 dataset #3


title: prostate tumour CPCG0453

description: new


title: VMP_scRNA_seq2_cell_85 dataset #3


title: prostate tumour CPCG0452

description: new


title: Prostate_tumour_CPCG0246_rep1 [re-analysis]


title: Prostate_tumour_CPCG0242_rep3 [re-analysis]


title: Prostate_tumour_CPCG0243_rep1 [re-analysis]


title: VMP_scRNA_seq2_cell_86 dataset #3


title: Prostate_tumour_CPCG0255_rep1 [re-analysis]


title: Prostate_tumour_CPCG0241_rep1 [re-analysis]


title: VMP_scRNA_seq2_cell_90 dataset #3


title: prostate tumour CPCG0451

description: new


title: Prostate_tumour_CPCG0242_rep2 [re-analysis]


title: VMP_scRNA_seq2_cell_96 dataset #3


title: prostate tumour CPCG0455

description: new


title: prostate tumour CPCG0439

description: new


title: VMP_scRNA_seq2_cell_83 dataset #3


title: VMP_scRNA_seq2_cell_82 dataset #3


title: Prostate_tumour_CPCG0238_rep1 [re-analysis]


title: prostate tumour CPCG0448

description: new


title: VMP_scRNA_seq2_cell_89 dataset #3


title: Prostate_tumour_CPCG0240_rep1 [re-analysis]


title: Prostate_tumour_CPCG0236_rep1 [re-analysis]


title: prostate tumour CPCG0445

description: new


title: VMP_scRNA_seq2_cell_77 dataset #3


title: Prostate_tumour_CPCG0235_rep1 [re-analysis]


title: prostate tumour CPCG0435

description: new


title: VMP_scRNA_seq2_cell_75 dataset #3


title: Prostate_tumour_CPCG0233_rep1 [re-analysis]


title: Prostate_tumour_CPCG0233_rep2 [re-analysis]


title: Prostate_tumour_CPCG0232_rep2 [re-analysis]


title: prostate tumour CPCG0434

description: new


title: Prostate_tumour_CPCG0242_rep1 [re-analysis]


title: prostate tumour CPCG0428

description: new


title: Prostate_tumour_CPCG0217_rep1 [re-analysis]


title: VMP_scRNA_seq2_cell_72 dataset #3


title: Prostate_tumour_CPCG0232_rep1 [re-analysis]


title: VMP_scRNA_seq2_cell_70 dataset #3


title: Prostate_tumour_CPCG0227_rep1 [re-analysis]


title: Prostate_tumour_CPCG0213_rep1 [re-analysis]


title: VMP_scRNA_seq2_cell_81 dataset #3


title: Prostate_tumour_CPCG0235_rep3 [re-analysis]


title: Prostate_tumour_CPCG0210_rep2 [re-analysis]


title: VMP_scRNA_seq2_cell_68 dataset #3


title: Prostate_tumour_CPCG0210_rep1 [re-analysis]


title: prostate tumour CPCG0406

description: new


title: Prostate_tumour_CPCG0235_rep2 [re-analysis]


title: prostate tumour CPCG0418

description: new


title: prostate tumour CPCG0423

description: new


title: VMP_scRNA_seq2_cell_67 dataset #3


title: VMP_scRNA_seq2_cell_66 dataset #3


title: prostate tumour CPCG0404

description: re-analysis of GSM2226279


title: prostate tumour CPCG0402

description: new


title: VMP_scRNA_seq2_cell_64 dataset #3


title: prostate tumour CPCG0397

description: new


title: VMP_scRNA_seq2_cell_61 dataset #3


title: VMP_scRNA_seq2_cell_63 dataset #3


title: Prostate_tumour_CPCG0208_rep1 [re-analysis]


title: VMP_scRNA_seq2_cell_57 dataset #3


title: Prostate_tumour_CPCG0191_rep2 [re-analysis]


title: Prostate_tumour_CPCG0203_rep1 [re-analysis]


title: Prostate_tumour_CPCG0189_rep3 [re-analysis]


title: Prostate_tumour_CPCG0189_rep2 [re-analysis]


title: Prostate_tumour_CPCG0200_rep1 [re-analysis]


title: Prostate_tumour_CPCG0208_rep2 [re-analysis]


title: Prostate_tumour_CPCG0191_rep1 [re-analysis]


title: Prostate_tumour_CPCG0189_rep1 [re-analysis]


title: Prostate_tumour_CPCG0190_rep1 [re-analysis]


title: Prostate_tumour_CPCG0196_rep1 [re-analysis]


title: prostate tumour CPCG0392

description: re-analysis of GSM2226278


title: Prostate_tumour_CPCG0188_rep1 [re-analysis]


title: Prostate_tumour_CPCG0187_rep1 [re-analysis]


title: prostate tumour CPCG0388

description: re-analysis of GSM2226277


title: Prostate_tumour_CPCG0185_rep1 [re-analysis]


title: Prostate_tumour_CPCG0184_rep2 [re-analysis]


title: Prostate_tumour_CPCG0196_rep2 [re-analysis]


title: VMP_scRNA_seq2_cell_54 dataset #3


title: VMP_scRNA_seq2_cell_53 dataset #3


title: prostate tumour CPCG0369

description: re-analysis of GSM2226276


title: Prostate_tumour_CPCG0184_rep1 [re-analysis]


title: VMP_scRNA_seq2_cell_44 dataset #3


title: Prostate_tumour_CPCG0183_rep1 [re-analysis]


title: prostate tumour CPCG0394

description: new


title: Prostate_tumour_CPCG0182_rep1 [re-analysis]


title: Prostate_tumour_CPCG0158_rep1 [re-analysis]


title: VMP_scRNA_seq2_cell_43 dataset #3


title: prostate tumour CPCG0345

description: re-analysis of GSM2226274


title: prostate tumour CPCG0271

description: new


title: Prostate_tumour_CPCG0154_rep1 [re-analysis]


title: prostate tumour CPCG0259

description: re-analysis of GSM2226273


title: VMP_scRNA_seq2_cell_33 dataset #3


title: Prostate_tumour_CPCG0114_rep1 [re-analysis]


title: Prostate_tumour_CPCG0117_rep1 [re-analysis]


title: Prostate_tumour_CPCG0127_rep1 [re-analysis]


title: Prostate_tumour_CPCG0132_rep1 [re-analysis]


title: Prostate_tumour_CPCG0102_rep1 [re-analysis]


title: VMP_scRNA_seq2_cell_37 dataset #3


title: prostate tumour CPCG0256

description: re-analysis of GSM2226272


title: VMP_scRNA_seq2_cell_32 dataset #3


title: VMP_scRNA_seq2_cell_30 dataset #3


title: Prostate_tumour_CPCG0099_rep1 [re-analysis]


title: Prostate_tumour_CPCG0100_rep2 [re-analysis]


title: Prostate_tumour_CPCG0094_rep1 [re-analysis]


title: Prostate_tumour_CPCG0087_rep1 [re-analysis]


title: prostate tumour CPCG0251

description: re-analysis of GSM2226271


title: VMP_scRNA_seq2_cell_29 dataset #3


title: prostate tumour CPCG0368

description: re-analysis of GSM2226275


title: Prostate_tumour_CPCG0100_rep1 [re-analysis]


title: Prostate_tumour_CPCG0078_rep2 [re-analysis]


title: prostate tumour CPCG0210

description: re-analysis of GSM2226214


title: VMP_scRNA_seq2_cell_27 dataset #3


title: VMP_scRNA_seq2_cell_28 dataset #3


title: Prostate_tumour_CPCG0083_rep1 [re-analysis]


title: Prostate_tumour_CPCG0078_rep1 [re-analysis]


title: prostate tumour CPCG0196

description: re-analysis of GSM2226212


title: VMP_scRNA_seq2_cell_26 dataset #3


title: Prostate_tumour_CPCG0073_rep2 [re-analysis]


title: Prostate_tumour_CPCG0073_rep1 [re-analysis]


title: Prostate_tumour_CPCG0072_rep1 [re-analysis]


title: prostate tumour CPCG0191

description: re-analysis of GSM2226211


title: Prostate_tumour_CPCG0057_rep1 [re-analysis]


title: prostate tumour CPCG0184

description: re-analysis of GSM2226210


title: Prostate_tumour_CPCG0047_rep1 [re-analysis]


title: prostate tumour CPCG0183

description: re-analysis of GSM2226209


title: VMP_scRNA_seq2_cell_25 dataset #3


title: Prostate_tumour_CPCG0048_rep1 [re-analysis]


title: VMP_scRNA_seq2_cell_19 dataset #3


title: VMP_scRNA_seq2_cell_23 dataset #3


title: Prostate_tumour_CPCG0040_rep1 [re-analysis]


title: Prostate_tumour_CPCG0040_rep2 [re-analysis]


title: Prostate_tumour_CPCG0027_rep1 [re-analysis]


title: prostate tumour CPCG0208

description: re-analysis of GSM2226213


title: prostate tumour CPCG0103

description: new


title: VMP_scRNA_seq2_cell_09 dataset #3


title: prostate tumour CPCG0100

description: new


title: VMP_scRNA_seq2_cell_05 dataset #3


title: VMP_scRNA_seq2_cell_04 dataset #3


title: Prostate_tumour_CPCG0007_rep1 [re-analysis]


title: prostate tumour CPCG0102

description: re-analysis of GSM2226208


title: prostate tumour CPCG0099

description: re-analysis of GSM2226207


title: VMP_scRNA_seq2_cell_02 dataset #3


title: VMP_scRNA_seq2_cell_01 dataset #3


title: VMP_scRNA_seq2_cell_65 dataset #3


title: VMP_scRNA_seq2_cell_55 dataset #3


title: VMP_scRNA_seq2_cell_16 dataset #3


title: VMP_scRNA_seq2_cell_35 dataset #3


title: VMP_scRNA_seq2_cell_03 dataset #3


title: VMP_scRNA_seq2_cell_17 dataset #3


title: VMP_scRNA_seq2_cell_18 dataset #3


title: VMP_scRNA_seq2_cell_52 dataset #3


title: VMP_scRNA_seq2_cell_13 dataset #3


title: VP_scRNA_seq_cell_95 dataset #3

description:
Rat_scRNAseq_Expr_Counts_VP1.txt
single-cell RNA sequencing Fluidigm C1


title: VP_scRNA_seq_cell_93 dataset #3


title: Lung tissue_treat rep2

city: Pyeongchang

first: Joonghoon

last: Park

state: Kangwon

address: Pyeongchang daero 1447

department: International Agricultural Technology

institute: Seoul National University

description:
LN02_treat
LN02_processed_data.txt

data_processing:
8oxoG-affinity purification sequencing
Image analysis and base calling were performed using the Illumina pipeline (v1.8) with default settings.
The reads were aligned to the mouse reference genome (mm8) with Isaac aligner (Illumina).
Duplicated reads were identified and removed with Picard (http://broadinstitute.github.io/picard/); enriched peaks were called from the mapped reads using MACS2 (Zhang et al. 2008), and peaks were annotated with ChIPseeker (Yu et al. 2015).
8-OxoG lesions differing significantly from those in input DNA (P < 10-4.5) were selected for further analyses.
Genome_build: mm8
Supplementary_files_format_and_content: Tab-delimited text files include pileup, (-)log10(-pvalue), fold_enrichment, and (-)log10(q-value) for each sample

source_name: Lung tissue_treat

extract_protocol:
DNA fragments harboring 8-oxoG were enriched as previously described (Ding et al. 2017), with minor modifications. Briefly, 5 µg of the genomic DNA extracted from adipose or lung tissues of randomly selected mice (n = 2) were sheared with an S2 ultrasonicator (Covaris, Woburn, MA, USA) in 10 mM Tris buffer (pH 8.0) to obtain ~150-bp fragments. After sonication, the fragmented DNA was concentrated to 20 µl in 100 mM NaPi buffer (pH 8.0) using QIAquick PCR purification kit (Qiagen). A 100-µl volume of 100 mM NaPi buffer containing 20 mM amine-PEG2-biotin (Thermo Fisher Scientific) was added and the mixture was heated to 75 °C for 10 min. After thermal equilibration, 5 mM K2IrBr6 was added for 1 h for 8-oxoG biotinylation. The DNA fragments biotinylated at 8-oxoG were eluted with 125 µl Tris buffer using the QIAquick PCR purification kit and extracted using Dynabeads MyOne Streptavidin C1 (Thermo Fisher Scientific); strands complementary to those with bound biotinylated 8-oxoG were released by incubation in 150 mM NaOH at 20 °C for 30 min, and concentrated to 10 µl ddH2O using ssDNA/RNA Clean & Concentrator kit (Zymo Research, Irvine, CA, USA).
The 8-oxoG-enriched DNA fragments obtained by affinity purification were subjected to next-generation sequencing. Libraries were constructed using the TruSeq Nano DNA kit (Illumina, San Diego, CA, USA) and sequenced with the TruSeq SBS Kit v3 on a HiSeq 2000 sequencer (Illumina) to obtain 101-bp paired-end reads.

value: female

value: Lung

value: 4 weeks old

tag: genotype

value: wild type

tag: treatment

value: Telmisartan 5 mg/kg/day


title: VP_scRNA_seq_cell_92 dataset #3


title: Lung tissue_input rep2

description:
LN02_input
LN02_processed_data.txt

source_name: Lung tissue_input


title: VP_scRNA_seq_cell_89 dataset #3


title: Lung tissue_treat rep1

description:
LN01_treat
LN01_processed_data.txt


title: VP_scRNA_seq_cell_87 dataset #3


title: Lung tissue_input rep1

description:
LN01_input
LN01_processed_data.txt


title: VP_scRNA_seq_cell_85 dataset #3


title: Adipose tissue_treat rep2

description:
F02_treat
F02_processed_data.txt

source_name: Adipose tissue_treat

value: Adipose


title: Adipose tissue_input rep2

description:
F02_input
F02_processed_data.txt

source_name: Adipose tissue_input


title: VP_scRNA_seq_cell_79 dataset #3


title: VP_scRNA_seq_cell_80 dataset #3


title: VMP_scRNA_seq2_cell_78 dataset #3


title: Blood_C24_control

city: São Paulo

first: Caroline

middle: Perez

last: Camilo

state: São Paulo

address: Rua Doutor Ovídio Pires de Campos, 785

department: Institute of Psychiatry

country: Brazil

institute: University of São Paulo

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to the Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

scan_protocol: Arrays were scanned in the iScan Microarray Scanner (Illumina Inc., San Diego, California, USA)

data_processing: Data processing were performed using GenomeStudio software (version 1.8).

label: Cy3, Cy5

source_name: DNA blood, Control 24, healthy control

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA from whole blood were extracted using salting-out method described by Miller and collaborators (Miller et al., Nucleic Acids Res., 1988;16(3):1215)

value: Male

value: Whole blood

tag: sample group

value: Healthy control

tag: ethnicity

value: African

tag: education

value: Secondary school

tag: smoke (use/abuse of other drugs)

tag: cannabbis (use/abuse of other drugs)

tag: solvents (use/abuse of other drugs)

tag: heroin (initial use/age ys)


title: Adipose tissue_treat rep1

description:
F01_treat
F01_processed_data.txt

tag: gender

tag: tissue


title: Blood_C12_control

source_name: DNA blood, Control 12, healthy control

tag: age

value: Caucasian

value: Primary school or less


title: Blood_C15_control

source_name: DNA blood, Control 15, healthy control


title: Adipose tissue_input rep1

description:
F01_input
F01_processed_data.txt


title: Blood_C19_control

source_name: DNA blood, Control 19, healthy control


title: VP_scRNA_seq_cell_78 dataset #3

value: Ventral prostate (VP)

value: P0 (day of birth)

value: Wistar


title: Blood_C23_control

source_name: DNA blood, Control 23, healthy control


title: Blood_C21_control

source_name: DNA blood, Control 21, healthy control


title: Blood_C13_control

source_name: DNA blood, Control 13, healthy control


title: Blood_C22_control

source_name: DNA blood, Control 22, healthy control


title: Blood_C11_control

source_name: DNA blood, Control 11, healthy control


title: VP_scRNA_seq_cell_74 dataset #3


title: Blood_C10_control

source_name: DNA blood, Control 10, healthy control


title: Blood_C8_control

source_name: DNA blood, Control 8, healthy control


title: VP_scRNA_seq_cell_65 dataset #3

source_name: Male urogenital sinus


title: VP_scRNA_seq_cell_71 dataset #3


title: Blood_C2_control

source_name: DNA blood, Control 2, healthy control


title: VP_scRNA_seq_cell_61 dataset #3


title: Blood_C5_control

source_name: DNA blood, Control 5, healthy control


title: Blood_C17_control

source_name: DNA blood, Control 17, healthy control


title: Mouse forelimb D5 rep3

description:
Mm_FL_D5_Rep3
processed data file:
mm_HTSeq_upload.txt

source_name: forelimb digit5

value: forelimb digit5


title: Blood_C4_control

source_name: DNA blood, Control 4, healthy control


title: Blood_C9_control

source_name: DNA blood, Control 9, healthy control


title: Blood_C3_control

source_name: DNA blood, Control 3, healthy control


title: Blood_C18_control

source_name: DNA blood, Control 18, healthy control


title: VP_scRNA_seq_cell_59 dataset #3


title: Blood_C7_control

source_name: DNA blood, Control 7, healthy control


title: VP_scRNA_seq_cell_58 dataset #3


title: VP_scRNA_seq_cell_77 dataset #3


title: VP_scRNA_seq_cell_56 dataset #3


title: Mouse forelimb D4 rep3

description:
Mm_FL_D4_Rep3
processed data file:
mm_HTSeq_upload.txt

source_name: forelimb digit4

value: forelimb digit4


title: Mouse forelimb D5 rep1

description:
Mm_FL_D5_Rep1
processed data file:
mm_HTSeq_upload.txt


title: VP_scRNA_seq_cell_55 dataset #3


title: Mouse forelimb D4 rep2

description:
Mm_FL_D4_Rep2
processed data file:
mm_HTSeq_upload.txt


title: Blood_C14_control

source_name: DNA blood, Control 14, healthy control


title: Blood_C20_control

source_name: DNA blood, Control 20, healthy control


title: Blood_C6_control

source_name: DNA blood, Control 6, healthy control