title: LPS/IL4/IL13_1

description:
Gene expression data from 6h of LPS/IL4/IL13 treatment
LPS IL4 IL13_1  (MoGene-1_0-st-v1).mas5-Signal


title: D6_P1__S21

status: Public on Oct 02 2019

type: SRA

city: Palo Alto

first: Michelle

last: Monje

state: CA

address: 265 Campus Drive Room 3035

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to the hg19 reference genome using bowtie version 0.12.7: bowtie -q --phred33-quals -n 1 -e 99999999 -l 25 -I 1 -X 2000 -a -m 15 --best -S -p 6
Cells expressing fewer than 200 genes and genes expressed by fewer than 3 cells were excluded from downstream analyses.
Reads for each cell were quantified and expressed as transcripts per million (TPM) using rsem version 1.2.19: rsem-calculate-expression --estimate-rspd --paired-end -sam -p 6
Genome_build: hg19
Supplementary_files_format_and_content: Processed TPM (non-log transformed) values for each cell  are compiled in a single matrix containing genes as rows and cells as columns. The column names of the TPM matrix reflect the cell line of sorted xenograft, the 96-well plate number and the well position within that plate. For instance D6_P1_S10 reflects a cell from the DIPG 6 xenograft, the first sorted plate and the 10th well in that plate

molecule: polyA RNA

organism: Homo sapiens

source_name: patient-derived DIPG cell line developed in the Monje Lab

growth_protocol: Patient-derived DIPGVI and DIPGXIII-FL cells were cultured as neurospheres in defined-medium before being dissociated to single cell suspension for xenografting into the mouse hippocampus.

extract_protocol:
Cells were extracted from the mouse brain using mechanical and enzymatic dissociation (Brain Tumor Dissociation Kit, Miltenyi)
Libraries were constructed following Illumina Nextera XT protocol and a dual-unique indexing strategy.
Nextera XT single cell RNA-seq

treatment_protocol: Cells were lentivirally transduced to constitutively express GFP protein and firefly luciferase.

tag: cell type

value: DIPG6 (VI) cell line

tag: passages

tag: disease state

value: DIPG (diffuse intrinsic pontine glioma)


title: PBMCs_healthy control_sample 3

type: RNA

city: Beijing

first: Liping

last: Pan

address: 97 Machang Road, Tongzhou District

country: China

institute: Beijing Chest Hospital, Capital Medical Universtiy.

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃, 20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US)

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US).

molecule: total RNA

source_name: peripheral blood mononuclear cells, healthy control, sample 3

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted from PBMCs using the miRNeasy® Mini kit (QIAGEN, Germany) according to the protocols recommended by the manufacturer.

tag: cell

value: peripheral blood mononuclear cells

tag: age

tag: gender

value: Male


title: PBMCs_healthy control_sample 4

source_name: peripheral blood mononuclear cells, healthy control, sample 4


title: LPS treated replicate 4

city: La Jolla

first: Antoni

middle: J

last: Duleba

address: 9500 Gilman Drive

department: Ob/Gyn

institute: University of California San Diego

description:
C4_LPS
C4L
mRNA
processed data file: readcount_Fox_et_al.csv

data_processing:
Raw FASTQ files were pre-processed to trim adapters.
Reads were mapped to the Rat genome using Tophat (2.1.1). Duplicate reads were removed from the BAM output using Samtools.
Read counts were generated using summarizeOverlapsCounts function and differential analysis done using DESeq2.
Genome_build: NCBI_Rnor_6.0
Supplementary_files_format_and_content: readcount_Fox_et_al.csv: Comma-separated read counts table.

organism: Rattus norvegicus

source_name: Isolated theca-interstitial cells

growth_protocol: Isolated thecal interstitial cells (TICs) were cultured on human fibronectin-coated plates in McCoys 5A culture medium at a density of 1-2x10^5 cells/well.

extract_protocol:
RNA was isolated using the MagMAX-96 Total RNA Isolation kit.
Illumina TruSeq Stranded mRNA kit.
RNAseq using Illumina HiSeq4000 sequencer.

treatment_protocol: TICs were incubated in the presence of vehicle (control) or in the presence of rat IL-1b and LPS (1µg/ml).

tag: strain

value: Sprague Dawley

tag: genotype

value: Wild type

tag: Sex

value: Female

value: Post-natal day 30

value: Theca-interstitial cells

tag: treatment

value: LPS


title: D6_P1__S29


title: LPS treated replicate 3

description:
C3_LPS
C3L
mRNA
processed data file: readcount_Fox_et_al.csv


title: SMS_CTR_RNA

city: Beaverton

first: Noah

last: Berlow

address: 12655 SW Beaverdam Rd

institute: CC-TDI

data_processing:
Raw reads aligned to GRCh38 human reference genome using STAR.
Aligned transcripts were quantified using RSEM.
Genome_build: GRCh38 human genome
Supplementary_files_format_and_content: *.txt: Result files are in tabular format. These files have quantified TPM data with additional information.

source_name: tumor

growth_protocol: DMEM + 10% FBS + 1% P/S.

extract_protocol:
RNA was isolated from snap frozen cells following harvesting from plateware. RNA isolation was performed at Beijing Genomics Institute.
Library construction was performed at Beijing Genomics Institute.
Paired-end RNA sequencing

treatment_protocol: No treatment conditions.

tag: tumor type

value: Embryonal rhabdomyosarcoma

tag: sample type

value: Established cell line

tag: cell line

value: SMS-CTR


title: D6_P1__S1


title: D6_P1__S20


title: TL-Om1_shEZH1_1

city: Minato-ku

first: Makoto

last: Yamagishi

state: Tokyo

address: 4-6-1, Shirokanedai

country: Japan

institute: The University of Tokyo

description: Gene expression_shEZH1

hyb_protocol: 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) for 1min and with GE Wash buffer 2 (Agilent) for 1min at 37°C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44K microarray slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel was set to Green, and No extended dynamic range was selected).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol : GE1-107_Sep09 and Grid: 026652_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng total RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted using TriZol (Invitrogen) following the manufacturer's recommendations. The protocol includes DNaseI treatment to eliminate any genomic DNA contamination. The extracted total RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: ATL cell line

tag: shRNA


title: PBMCs_healthy control_sample 1

source_name: peripheral blood mononuclear cells, healthy control, sample 1


title: PBMCs_healthy control_sample 2

source_name: peripheral blood mononuclear cells, healthy control, sample 2


title: D6_P1__S19


title: PBMCs_VM patient_sample 4

source_name: peripheral blood mononuclear cells, VM patient, sample 4


title: HS729TA


title: 7927554038_R01C02: DNA methylation from saliva

type: genomic

city: Munich

first: Binder

last: Elisabeth

address: Kraepelinstr. 2+10

country: Germany

institute: Max-Planck-Institute Psychiatry

hyb_protocol: as recommended by Illumina

scan_protocol: as recommended by Illumina

data_processing: as recommended by Illumina

label: Cy3, Cy5

molecule: genomic DNA

source_name: saliva

label_protocol: as recommended by Illumina

extract_protocol: DNAdvance kit, Beckman Coulter Genomics

value: female

tag: tissue

value: saliva


title: D6_P1__S18


title: IL4/IL13_2

city: Calgary

first: Manoj

middle: Kumar

last: Mishra

state: AB

address: 3330 Hospital Dr NW

department: Clinical Neuroscience

country: Canada

institute: Hotchkiss Brain Institute

description:
Gene expression data from 6h of IL4/IL13 treatment
IL4 IL13_2  (MoGene-1_0-st-v1).mas5-Signal

hyb_protocol: Following fragmantation, hybridized to an Affymetrix GeneChip™ Mouse Gene 1.0 ST Array  at 45 °C for 16 h.

scan_protocol: Scanned with Affymetrix GeneChip Scanner 3000 7G System.

data_processing: Array data files were generated with GeneChip Command Console Software (AGCC) and statistical significant analysis was carried out on software of GeneSpring (Agilent Technologies). The fold change between treatment and control was based on the P < 0.05 from unpaired t test (Asymptotic and Benjamini Hochberg FDR).

label: biotin

organism: Mus musculus

source_name: BMDM exposed to IL4/IL13

label_protocol: 100 μg of RNA of each sample with a RIN higher than 9 was labeled with the 3′ _IVT Express Kit (Ambion)

extract_protocol: RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) according to the manufacturer’s protocol. Total RNA was purified with the RNeasy Plus Micro Kit (Qiagen) to remove genomic DNA. The RNA quality of integrity number (RIN) was measured with an Agilent RNA 6000 NanoChip on 2100 Bioanalyzer (Agilent Technologies).

value: bone marrow derived cells (BMDM)

value: exposed to IL4/IL13


title: LPS treated replicate 1

description:
C1_LPS
C1L
mRNA
processed data file: readcount_Fox_et_al.csv


title: 7959804122_R05C02: DNA methylation from saliva

value: male


title: IL1b treated replicate 4

description:
B4_IL1b
B4I
mRNA
processed data file: readcount_Fox_et_al.csv


title: PBMCs_VM patient_sample 3

source_name: peripheral blood mononuclear cells, VM patient, sample 3

value: peripheral blood mononuclear cells


title: RMS13_RNA

growth_protocol: RPMI + 10% FBS + 1% P/S.

value: Rhabdomyosarcoma


title: 7959804122_R03C02: DNA methylation from saliva


title: D6_P1__S16

value: DIPG6 (VI) cell line

value: DIPG (diffuse intrinsic pontine glioma)


title: CCA_RNA

value: CCA


title: 7927554029_R01C01: DNA methylation from saliva


title: D6_P1__S17


title: 7927554004_R04C01: DNA methylation from saliva


title: PBMCs_VM patient_sample 1

source_name: peripheral blood mononuclear cells, VM patient, sample 1

value: Male


title: D6_P1__S15


title: RH18_RNA

growth_protocol: Not provided

extract_protocol: Paired-end RNA sequencing

value: Alveolar rhabdomyosarcoma


title: 7927554006_R05C02: DNA methylation from saliva


title: RD_RNA

value: RD


title: PBMCs_VM patient_sample 2

source_name: peripheral blood mononuclear cells, VM patient, sample 2

value: Female


title: PBMCs_TBM patient_sample 4

source_name: peripheral blood mononuclear cells, TBM patient, sample 4


title: 7927554029_R03C01: DNA methylation from saliva


title: IL1b treated replicate 2

description:
B2_IL1b
B2I
mRNA
processed data file: readcount_Fox_et_al.csv

value: Sprague Dawley

value: Wild type

value: Post-natal day 30

value: Theca-interstitial cells


title: D6_P1__S14


title: CW9019_RNA

value: Established cell line


title: IL1b treated replicate 1

description:
B1_IL1b
B1I
mRNA
processed data file: readcount_Fox_et_al.csv


title: PBMCs_TBM patient_sample 3

source_name: peripheral blood mononuclear cells, TBM patient, sample 3


title: Control-replicate4

description:
A4_Control
A4C
mRNA
processed data file: readcount_Fox_et_al.csv

value: Control


title: 7927554023_R05C01: DNA methylation from saliva

value: saliva


title: D6_P1__S13


title: PBMCs_TBM patient_sample 2

source_name: peripheral blood mononuclear cells, TBM patient, sample 2


title: 7927554006_R01C02: DNA methylation from saliva

value: female


title: IL1b treated replicate 3

description:
B3_IL1b
B3I
mRNA
processed data file: readcount_Fox_et_al.csv


title: COG-R-486H_RNA

growth_protocol: DMEM + 20% FBS in hypoxic conditions.

value: Rhabdomyosarcoma (not otherwise specified)


title: Control-replicate3

description:
A3_Control
A3C
mRNA
processed data file: readcount_Fox_et_al.csv


title: Control-replicate2

description:
A2_Control
A2C
mRNA
processed data file: readcount_Fox_et_al.csv


title: RMS559_RNA

value: Embryonal rhabdomyosarcoma


title: D6_P1__S11

value: DIPG6 (VI) cell line


title: PCB-234_RNA

growth_protocol: No growth conditions.

extract_protocol:
RNA was isolated from preserved clinical tissue stored as cryopreserved tissue or FFPE tissue. RNA isolation was performed at OHSU Genomic Profiling Shared Resource.
Library construction was performed at OHSU Sequencing Core.
Paired-end RNA sequencing

value: Primary tissue


title: D6_P1__S12

value: DIPG (diffuse intrinsic pontine glioma)


title: Control-replicate1

description:
A1_Control
A1C
mRNA
processed data file: readcount_Fox_et_al.csv


title: Stard5-EGFP/Rpl10a-JX5852, Ventral striatum, IP Rep2

city: New York

first: Laura

last: Kus

state: NY

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

data_processing:
FASTX Toolkit 0.0.13 was used to assess the quality of reads and trim trailing adaptors.
Trimmed reads were aligned to annotated exons using the mm10 genome using STAR v2.0.0e_r291 using default settings.
Raw counts of mapped reads were generated with HTSeq framework v0.6.0 using the htseq-count module with the "union" mode and default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of counts

source_name: Ventral striatum

growth_protocol: Not applicable

extract_protocol:
The ventral striatum was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

treatment_protocol: Control mice only. No treatment

value: Ventral striatum

tag: animal line

value: Stard5-TRAP JX5852

tag: application

value: RNA-seq

tag: antibody

value: monoclonal anti-EGFP


title: PBMCs_TBM patient_sample 1

source_name: peripheral blood mononuclear cells, TBM patient, sample 1

value: peripheral blood mononuclear cells

value: Female


title: PCB-00082_RNA


title: 7927554038_R05C01: DNA methylation from saliva


title: 7959804122_R04C02: DNA methylation from saliva


title: 7927554006_R03C02: DNA methylation from saliva


title: SMYD-KO

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

data_processing:
FASTX-Toolkit (Gordon and Hannon, 2010) was used to remove adapters and reads of low quality from the raw data, after which the remaining reads were mapped onto the Tetrahymena thermophila genome (http://ciliate.org/index.php/home/downloads, June 2014) by Bowtie2 (v2.2.5) and gene expression levels were calculated by RSEM v1.2.7 (Li and Dewey, 2011).
Genome_build: T_thermophila_June2014_assembly

organism: Tetrahymena thermophila

source_name: ΔSMYD

growth_protocol: 10ml of wide type cells and SMYD knockout cells were cultured in 1XSPP medium and harvested at 2x10^5 cells/ml.

extract_protocol:
Total RNA of log-phased △SMYD1 and wild-type CU428 cells (negative control) were extracted using Qiashredder (Qiagen, 79654) and RNeasy Kit (Qiagen, 74624) according to protocol provided in TetraFGD (Xiong et al., 2013). Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, CA, USA, Q32852) and RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA, 5067-1511) were used to measure the RNA concentration and integrity, respectively
RNA libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol for RNA-seq libraries.

treatment_protocol: In SMYD knockout strain, SMYD gene was knocked out by particle bombardment.

value: SMYD-KO

tag: cell type

value: log phased cells


title: WT

value: WT


title: Rh5_RNA

value: Alveolar rhabdomyosarcoma

value: Established cell line


title: Stard5-EGFP/Rpl10a-JX5852, Ventral striatum, IP Rep1


title: CF130_RNA

extract_protocol:
RNA was isolated from preserved clinical tissue stored as cryopreserved tissue or FFPE tissue. RNA isolation was performed at Beijing Genomics Institute.
Library construction was performed at Beijing Genomics Institute.
Paired-end RNA sequencing


title: OSC SiCOSMOC Individual 1 (C1) replica 2

status: Public on Oct 01 2019

city: Marseille

first: Madeleine

last: Erard-Garcia

address: 51 Blvd Pierre Dramard

country: France

institute: 1UMR 7051, INP, CNRS and Aix-Marseille University

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

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the GCS3000 7G system.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: GeneChip CEL files were analyzed using GeneSpring (Agilent Technologies). The log2 values were obtained and the microarray data were normalized using RMA16 algorithm. Gene level was investigated. Statistical data analyses were done on all samples for each group. Similarly, enrichment rankings are based on all samples per group. Data were filtered with GeneSpring analysis using a cutoff of at least 1.3× up or down (Fold change 1.3, FC1.3). Subsequently, one-way ANOVA was performed on a filtered list. The Benjamini–Hochberg false discovery rate (FDR) was set to 5%, and the P value was set to < 0.05 (ANOVA test). The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was used to find gene ontology-enriched terms.

label: Biotin

source_name: Healthy Individuals

label_protocol: Genome-wide transcriptional profiling was performed by Human Exon 1.0 ST arrays (Affymetrix) following manufacturer’s instructions. Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Cells were used at a low passage number (P10 maximum) and were regularly controlled as free of mycoplasma contamination throughout the study. Primary OSCs as well as SH-SY5Y, U138-MG, HepG2, HEK-293 and Caco-2 cell lines were cultured with DMEM high glucose media containing Glutamax media (Life Technologies) and supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. THP-1 cells were cultured with RPMI media (Life Technologies), 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were incubated at 37°C in a humidified chamber containing 5% CO2. Culture media was changed every three days and cells were passaged with Trypsin/EDTA (Life Technologies) when they reached ~90% confluency.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manifacturer’s instruction.

treatment_protocol: Twenty-four hours after seeding, cells were transfected with Stealth RNAi™ siRNAs (Life Technologies) using Lipofectamine RNAimax (Life Technologies). Experiments using Stealth RNAi™ siRNA negative controls (Life Technologies) were performed in parallel.

value: Human nasal olfactory stem cells (OSC)

tag: genotype/variation

value: siRNA against the lncRNA COSMOC


title: OSC SiCOSMOC Individual 1 (C1) replica 1


title: OSC SiCOSMOC Individual 2 (C2) replica 2


title: OSC SiCOSMOCIndividual 2 (C2) replica 1


title: 7927554004_R02C01: DNA methylation from saliva

value: male

value: saliva


title: OSC Ctrl Individual 2 (C2) replica 1

value: control


title: LPS treated replicate 2

description:
C2_LPS
C2L
mRNA
processed data file: readcount_Fox_et_al.csv

source_name: Isolated theca-interstitial cells

value: Sprague Dawley

value: Wild type

value: Post-natal day 30

value: Theca-interstitial cells

value: LPS


title: OSC Ctrl Individual 1 (C1) replica 1


title: OSC Ctrl Individual 1 (C1) replica 2


title: 09.5.19 P

city: Chang Sha

first: Hao

address: Xiangya NO.72

department: Department of Periodontics

institute: Xiangya Stomatological Hospital & School of Stomatology, Central South University

description: RNA from tumor tissues of patients with OSCC

hyb_protocol: The labled RNA were hybridized for 16 hr at 48C on Affymetrix miRNA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed with mRNA QCTool using Affymetrix default analysis settings and quantile as normalization method.

source_name: tongue

label_protocol: About 1ug total RNA were polyA tailed and labled with FlashTag™ Biotin HSR Labeling Kit. This kit can be used to label any RNA sample, including total RNA, severely degraded RNA, plant RNA, and low molecular weight RNA.

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

treatment_protocol: Paired primary tumor tissues were obtained from patients with OSCC. The tumor tissues were obtained from surgical excision. All tissues were snap-frozen in liquid  nitrogenat at -80C until use.

tag: patient id

tag: patient diagnosis

value: Oral squamous cell carcinoma (OSCC)

value: oral mucous

tag: tumor location

value: tongue

tag: tissue disease state

value: tissue adjacent to cancer


title: 09.6.1 Ca

value: cancer

tag: gender


title: 09.7.27 N

value: contralateral normal


title: 09.7.20 N

source_name: oral buccal

value: oral buccal


title: 09.7.20 Ca


title: 09.5.19 N


title: 09.7.28 N

value: female


title: 09.7.27 P


title: 09.7.27 Ca


title: 09.7.28 Ca


title: 09.6.1 N


title: 09.7.28 P


title: 09.6.1 P


title: 09.7.20 p


title: 09.6.22 N


title: 09.6.22 Ca


title: 09.5.19 Ca


title: 09.6.22 P


title: MCF7 cells untreated-rep2

city: Atlanta

first: Jonathan

last: Mitchel

state: GA

address: 315 Ferst Drive

department: School of Biological Sciences

institute: Georgia Institute of Technology

hyb_protocol: Hybridization for 18 hours at 45C with rotation

scan_protocol: GeneChipnScanner 3000 High resolution scanning, HG_U133 Plus 2.0 library files.

data_processing: The data were analyzed using affy R package and preprocessed using RMA

source_name: MCF7 cells, untreated

label_protocol: Total RNA was biotin labeled with GeneChip 3' IVT plus KIT (Appliedbiosystems)

growth_protocol: MCF7 cells were cultured in RPMI 1640 with 1% antibiotic-antimycotic solution. The cells were deprived of serum for 24 hours before treatment.

extract_protocol: Total RNA was extracted from cells using the RNeasy Mini Kit

treatment_protocol: MCF7 cells were treated with 9 µM GW4064 or vehicle (.3% DMSO) for 24 hours before RNA isolation.

value: MCF7 cell line of breast adenocarcinoma


title: MCF7 cells untreated-rep3


title: MCF7 cells GW4064 treated-rep1

source_name: MCF7 cells, treated with 9 µM GW4064


title: MCF7 cells GW4064 treated-rep2


title: Patient, biological rep2

city: Pozzuoli

first: Diego

last: Carrella

state: NAPOLI

address: Via Campi Flegrei 34

country: Italy

institute: TIGEM

description: Gene expression data in human kidney tubule epithelial from patient with MMA

hyb_protocol: Hybridization and scanning was performed on the Affymetrix platform.

data_processing: The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.

source_name: human kidney

label_protocol: Oligo(dT)-primed cDNAs were synthesized using the SuperScript III First-Strand Synthesis SuperMix (Invitrogen, Irvine, CA) following manufacturer’s instructions. For microarray analysis, double-stranded cDNAs were synthesized using the Custom SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and extracted with phenol-chloroform isoamyl alcohol (25:24:1), ethanol precipitated, and used to prepare cRNAs using the Bioarray High Yield RNA Transcription Kit (Affymetrix, Santa Clara, CA) according to manufacturer’s instructions.

growth_protocol: Tubular epithelial cells were purified from urine of healthy donors and patients with MMA and cultured in a selective medium containing Dulbecco’s Modified Eagle Medium and Ham’s F12 medium. It was supplemented with fetal calf serum, insulin, hydrocortisone, selenite, transferrin, hEGF, NAD and 3,3,5 triiodo-L-thyronine. Confluent cells were sub–cultivated until 3rd passage and, subsequently, immortalized using pRSVneo vector containing SV40 DNA (pRNS1). Afterwards, immortalized kidney tubule epithelial cells were characterized for protein expression and enzyme activity.

extract_protocol: Total RNA was extracted from cell cultures with RNAqueous R kit (Applied Biosystems, Life Technologies).

treatment_protocol: The cells were kept in cell growth medium for 72 hours

value: human kidney

tag: disease

value: Methylmalonic acidemia (MMA)


title: MCF7 cells untreated-rep1


title: Patient, biological rep1

scan_protocol: Hybridization and scanning was performed on the Affymetrix platform.


title: MCF7 cells GW4064 treated-rep3


title: Patient, biological rep3


title: Control, biological rep1

description: Gene expression data in human kidney tubule epithelial from heathy control

value: heathy


title: Control, biological rep3


title: CHC379T (HCA)

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

institute: Centre de Recherche des Cordeliers

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_0379T_U133_2

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Raw data were obtained by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Santa Clara, USA). Background subtraction, normalization and expression summaries for every probe set were calculated with the log-scale robust multi-array analysis (RMA) algorithm.

source_name: Hepatocellular Adenoma

label_protocol: Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2007, Affymetrix)

extract_protocol: RNA samples were extracted from frozen tissues, in accordance with standard procedures, as previously described [Rebouissou et al. J Biol Chem 2007]

value: Hepatocellular Adenoma

tag: disease state

value: Solid Tumor

value: Female

tag: age

tag: nb nodules

tag: metavir

tag: molecular subgroup

value: IHCA


title: CHC605T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_0605T_U133_2

tag: tissue

value: shHCA


title: CHC603T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_0603T_U133_2


title: CHC967T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_0967T_U133_2

value: bHCA


title: CHC582T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_0582T_U133_2


title: CHC635T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_0635T_U133_2.2

value: H-HCA


title: CHC358T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_0358T_U133_2.2


title: CHC535T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_0535T_U133_2.2


title: CHC1259T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_1259T_U133_2.2


title: CHC353T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_0353T_U133_2

value: UHCA


title: Control, biological rep2


title: CHC663T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_0663T_U133_2


title: CHC846T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_0846T_U133_2


title: CHC364T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_0364T_U133_2.2

value: bIHCA


title: CHC870T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_0870T_U133_2


title: CHC949T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_0949T_U133_2


title: CHC537T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_0537T_U133_2


title: CHC1666T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_1666T_U133_2.2


title: CHC1386T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_1386T_U133_2.2

value: IHCAM


title: CHC1439T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_1439T_U133_2

value: IHCANM


title: CHC1419T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_1419T_U133_2


title: CHC1380T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_1380T_U133_2


title: CHC1351T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_1351T_U133_2


title: CHC1346T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_1346T_U133_2


title: CHC1358T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_1358T_U133_2


title: CHC1365T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_1365T_U133_2


title: CHC1383T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_1383T_U133_2


title: D6_P1__S10

source_name: patient-derived DIPG cell line developed in the Monje Lab

extract_protocol:
Cells were extracted from the mouse brain using mechanical and enzymatic dissociation (Brain Tumor Dissociation Kit, Miltenyi)
Libraries were constructed following Illumina Nextera XT protocol and a dual-unique indexing strategy.
Nextera XT single cell RNA-seq

value: DIPG6 (VI) cell line

tag: passages

value: DIPG (diffuse intrinsic pontine glioma)


title: CHC1343T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_1343T_U133_2


title: CHC1337T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_1337T_U133_2


title: CHC1124T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_1124T_U133_2.2

value: Male


title: CHC1217T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_1217T_U133_2


title: CHC1123T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_1123T_U133_2.2


title: CHC562N (normal liver)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_0562N_U133_2

source_name: Non tumor liver

value: Non tumor liver


title: CHC1023T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_1023T_U133_2.2


title: DLD1 Glc+Gln

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: DLD1 under glucose- and glutamine-containing conditions

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: DLD1 and HT29 cells were cultured in complete medium; the medium was replaced the following day with glucose(−) and glutamine(−) medium supplemented with 10% dialysed fetal bovine serum. Glucose (10 mM) or glutamine (2 mM) was added, respectively. After 24 h incubation, cellular RNA was extracted.

extract_protocol: Total cellular RNA was purified from cultured cells using the RNeasy mini kit (Qiagen, Valencia, CA, USA) following the manufacturer’s protocol.

value: colorectal cancer

tag: cell line

tag: condition


title: DLD1 Gln

source_name: DLD1 under glucose-deprived conditions

value: glucose-deprived conditions


title: CHC1317T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_1317T_U133_2

value: Hepatocellular Adenoma


title: CHC469N (normal liver)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_0469N_U133_2


title: OSC Ctrl Individual 2 (C2) replica 2

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

value: Human nasal olfactory stem cells (OSC)

value: control


title: CHC934N (normal liver)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_0934N_U133_2


title: HT29 Gln

source_name: HT29 glucose-deprived conditions


title: HT29 Glc+Gln

source_name: HT29 under glucose- and glutamine-containing conditions


title: CHC1342T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_1342T_U133_2.2

value: Solid Tumor

value: Female


title: Brain tissue, Control, 703_10B

city: Oslo

first: Ståle

last: Nygård

address: Institute for Experimental Medical Research, Oslo University Hospital - Ulleval

country: Norway

institute: University of Oslo

description: Tissue from left central lobe of the brain

hyb_protocol: The assay probe sets consist of an upstream oligo containing a gene-spesific sequence and a universal PCR primer sequence at the 5’ end, and a downstream oligo containing a gene-specific sequence and a universal PCR primer sequence at the 3’. The upstream oligo hybridizes to the targeted cDNA site, and then extends and ligates to its corresponding downstream oligonucleotide to create a PCR template that can be amplified with universal PCR primers.

scan_protocol: Following washing and staining, the BeadChips were imaged using the Illumina iScan Reader to measure fluorescence intensity at each probe.

data_processing: After scanning, the iScan software extracts signal intensities and saves all files for each BeadChip. Raw data is imported to Illumina’s GenomeStudio software V2011.1, Gene Expression module v. 1.9.0. Background correction with bgAdjust.affy in lumi R/Bioconductor package. Quantile normalization, where the three tissue types where quantile normalized separately.

source_name: Brain tissue

label_protocol: The Whole-Genome DASL HT Assay begins with conversion of total RNA to cDNA using biotinylated oligo dT and random nonamer primers. The cDNA is then annealed to the DASL Assay Pool probe groups. Probe groups contain oligonucleotides specifically designed to interrogate each target sequence in the transcripts. These probes span about 50 bases, making it possible to profile partially degraded RNA

extract_protocol: Total RNA from 10-20 mg fresh frozen tissues were prepared using the RNeasy mini kits (Qiagen, Valencia, CA) following manufacturer’s instructions. The concentrations of the samples were measured using the NanoDrop Spectrophotometer. The integrity of the samples was assessed using the Agilent 2100 Bioanalyzer. For each sample, 400 ng of total RNA was amplified and labeled. Samples were distributed and processed in a 96-well format and were hybridized to Illumina HumanHT-12 v4 Expression BeadChips. Some samples were up-concentrated using vacuum drying to achieved required concentration/volume.

treatment_protocol: Tissue was harvested during autopsy and stored in RNA later in -70C untill analysis.

value: Control

value: Brain

value: 2 weeks

value: female


title: CHC966T (HCA)

description:
Gene expression data from hepatocellular carcinoma using Affy U133plus v2
JZN_0966T_U133_2

value: IHCA


title: Brain tissue, Control, 302_12B

value: male


title: Brain tissue, Control, 014_12B

value: 144 weeks


title: Brain tissue, Control, 603_10B

value: 52 weeks


title: Brain tissue, Infection, 412_11B

value: Infection

value: 24 weeks


title: Brain tissue, Infection, 219_12B

value: 60 weeks


title: Brain tissue, Control, 390_09B

value: 0 weeks


title: Brain tissue, Infection, 272_11B


title: Brain tissue, Infection, 834_10B


title: Brain tissue, Control, 098_10B


title: Brain tissue, Infection, 680_09B

value: 0.6 weeks


title: Brain tissue, Infection, 209_10B

value: 72 weeks


title: Brain tissue, Control, 625_08B


title: Brain tissue, Infection, 180_09B

value: 36 weeks


title: Brain tissue, Infection, 241_09B

value: 20 weeks


title: Brain tissue, Infection, 377_09B


title: Brain tissue, Control, 267_10B


title: Liver tissue, Control, 849_10L

description: Tissue from liver

source_name: Liver tissue

value: Liver


title: Brain tissue, Infection, 018_09B

value: 8 weeks


title: Liver tissue, Control, 1083_11

description: Tissue from liver

value: Control

value: 80 weeks


title: Liver tissue, Control, 737_09L

description: Tissue from liver

value: female


title: Liver tissue, Control, 905_10L

description: Tissue from liver


title: Liver tissue, Control, 267_10L

description: Tissue from liver


title: Liver tissue, Control, 681_08L

description: Tissue from liver


title: Liver tissue, Control, 365_12L

description: Tissue from liver

value: 2 weeks


title: Liver tissue, Control, 014_12L

description: Tissue from liver

value: male


title: Liver tissue, Infection, 123_11L

description: Tissue from liver


title: Liver tissue, Control, 603_10L

description: Tissue from liver


title: Liver tissue, Infection, 834_10L

description: Tissue from liver


title: Liver tissue, Infection, 209_10L

description: Tissue from liver


title: Liver tissue, Control, 098_10L

description: Tissue from liver


title: Liver tissue, Infection, 862_09L

description: Tissue from liver

value: 12 weeks


title: Liver tissue, Infection, 412_11L

description: Tissue from liver


title: Liver tissue, Infection, 180_09L

description: Tissue from liver


title: Liver tissue, Infection, 241_09L

description: Tissue from liver


title: Liver tissue, Infection, 377_09L

description: Tissue from liver


title: Liver tissue, Infection, 680_09L

description: Tissue from liver


title: Liver tissue, Infection, 018_09L

description: Tissue from liver


title: Heart tissue, Control, 849_10H

description: Tissue from the apex of the heart

source_name: Heart tissue

value: Heart


title: Brain tissue, Control, 681_08B

value: Brain


title: Heart tissue, Control, 1083_11

description: Tissue from the apex of the heart


title: Heart tissue, Control, 014_12H

description: Tissue from the apex of the heart

value: 144 weeks


title: Heart tissue, Control, 267_10H

description: Tissue from the apex of the heart


title: Heart tissue, Control, 098_10H

description: Tissue from the apex of the heart


title: A3_WT_I3

city: Irapuato

first: Manuel

last: Villalobos-Escobedo

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León Irapuato

department: Ingeniera Genetica

country: Mexico

institute: cinvestav

data_processing:
The sequences were mapped in the predicted transcripts in the genome of T. atroviride v2 from the JGI page (http://genome.jgi.doe.gov/Triat2/Triat2.home.html) using the Salmon software (Patro et al., 2017) and for A. thaliana, the version 10 of the genome obtained from TAIR was used for this mapping (https://www.arabidopsis.org/).
Differential expression analysis was done with the edgeR package (Robinson et al., 2010), using transcripts that at least had three counts per million in some library and a total of no less than 5 counts per million in all libraries. The counts matrix was normalized by trimmed mean of M-values method (TMM) (Robinson & Oshlack, 2010). The genes differentially expressed between the different conditions was determined using the method "Generalized linear model (GLM) likelihood radio test" (McCarthy et al., 2012). An FDR ≤ 0.05 was considered statistically significant in this analysis. A Fold-change =1 was put as a filter for differential genes.
Supplementary_files_format_and_content: counts

organism: Arabidopsis thaliana

source_name: Arabidopsis with wild-type strain 3 dpi

growth_protocol:
The Arabidopsis seeds had previously been sterilized and subjected to a vernalization period of 2 days, at 4 ° C in darkness. Once seeded, they were sealed and incubated in a growth chamber at 24 °C, with a photoperiod of 16 h in constant light (200 μmolm2s-1) per 8 h in darkness. After four days 1x106 spores of the respective strains were inoculated 5 cm away from seedlings. At 3 and 5 days after the inoculation (dpi), both mycelium and roots were collected to obtain the RNA.
Trichoderma was grown in MS medium. The RNA of the fungus was extracted from the mycelium closest to the root of Arabidopsis at 3 dpi and at 5 dpi when there is already contact between the fungus and the plant. As a control of this experiment, the fungus was grown without the presence of Arabidopsis at 5 dpi.

extract_protocol:
The extraction of RNA from the mycelium of T. Atroviride and the root of the plant was also done with the TRIZOL protocol (INVITROGEN).
The cDNA synthesis was performed according to the TruSeq® RNA Sample Preparation v2 Guide protocol and the sequencing was done on the Illumina HiSeq 2000 platform, in a 2X100 format.

value: root

tag: treatment

value: interaction with the fungus

tag: replicates

value: biological replica 3


title: Heart tissue, Control, 603_10H

description: Tissue from the apex of the heart

value: 52 weeks


title: A3_OA_C3

source_name: Only Arabidopsis growing 3 dpi (without Trichoderma)

value: control


title: A3_NR_I5

source_name: Arabidopsis with noxR mutant 5 dpi


title: Heart tissue, Control, 703_10H

description: Tissue from the apex of the heart

value: 0.5 weeks


title: Heart tissue, Infection, 123_11H

description: Tissue from the apex of the heart

value: Infection


title: Heart tissue, Control, 390_09H

description: Tissue from the apex of the heart

value: 0 weeks


title: A2_WT_I5

source_name: Arabidopsis with wild-type strain 5 dpi

value: biological replica 2


title: A3_NR_I3

source_name: Arabidopsis with noxR mutant 3 dpi


title: Heart tissue, Infection, 120_11H

description: Tissue from the apex of the heart

value: 24 weeks


title: A3_OA_C5

source_name: Only Arabidopsis growing 5 dpi (without Trichoderma)


title: Heart tissue, Control, 737_09H

description: Tissue from the apex of the heart

value: Control


title: Heart tissue, Infection, 241_09H

description: Tissue from the apex of the heart

value: 20 weeks


title: Heart tissue, Infection, 209_10H

description: Tissue from the apex of the heart

value: 72 weeks

value: male


title: Heart tissue, Infection, 180_09H

description: Tissue from the apex of the heart

value: Heart

value: 36 weeks


title: A2_WT_I3


title: Heart tissue, Infection, 412_11H

description: Tissue from the apex of the heart


title: Heart tissue, Infection, 018_09H

description: Tissue from the apex of the heart

value: 8 weeks

value: female


title: Heart tissue, Infection, 932_08H

description: Tissue from the apex of the heart

value: 112 weeks


title: Heart tissue, Infection, 377_09H

description: Tissue from the apex of the heart


title: Heart tissue, Infection, 680_09H

description: Tissue from the apex of the heart

value: 0.6 weeks


title: A3_WT_I5

value: root

value: interaction with the fungus

value: biological replica 3


title: A2_OA_C5

value: control


title: A2_OA_C3


title: Heart tissue, Control, 905_10H

description: Tissue from the apex of the heart


title: A2_NR_I5


title: A1_WT_I5

value: biological replica 1


title: A1_OA_C3


title: A1_OA_C5


title: A1_NR_I5


title: A1_NR_I3


title: Col+Cd.bam

city: Jinan

first: Xiangpei

last: Kong

address: 27 Shanda South Road

institute: Shandong University

data_processing:
The RNA was purified by electrophoresis through a TBE-urea polyacrylamide gel. The gel regions harboring 18-30 nt fragments were excised and the RNA recovered. The resulting population of sRNAs was 5' and 3' RNA adapter-ligated using T4 RNA ligase, and amplified for 18 PCR cycles
The amplicons were purified and sequenced using an Illumina/Solexa Genome Analyzer (Beijing Genomics Institute, Shenzhen, China).
Raw reads were trimmed by removing low-quality and adaptor sequences, then aligned to the A. thaliana genome using SOAP2 software.
Transcript frequency was calculated using the reads per kilobase per million reads method. Differentially transcribed genes were identified using a method modified from Audic and Claverie (1997). Significance was based on the P value and the false discovery rate (FDR) (Audic and Claverie, 1997).

source_name: root tip

growth_protocol: Total RNA was extracted from the root of 5-day-old Col-0 and the ein3-1eil1-1 mutant seedlings grown on MS medium, which were subsequently subjected to 150 μM CdSO4 for 6 h.

extract_protocol:
Root tips were cut, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent (Invitrogen, Carlsbad, CA, USA).
Total RNA was extracted from the shoots and roots with TRIZOL reagent (Invitrogen, Carlsbad, CA, USA). First strand cDNA was generated using reverse transcriptase and random primers. The constructed cDNA libraries was qualified and quantified with Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System, and then sequenced via Illumina HiSeqTM 2000 or other sequencer when necessary at the Beijing Genomics Institute, Shenzhen, China.

value: primary root

tag: genotype/variation

value: Col

value: 150 μM CdSO4 for 6 h


title: A1_WT_I3


title: Col.bam


title: ein3eil1.bam

value: ein3eil1 mutant


title: PUMPKIN rep2

city: Strasbourg

first: Kamel

last: Hammani

address: 12 Rue du général Zimmer

institute: IBMP-CNRS

data_processing:
Raw data were imported into CLC Genomics Workbench (Version): File -> Import -> Illumina with the following parameters: Discard quality scores = No, Paired orientation = Paired reads (forward-reverse), Minimum distance = 100, Maximum distance = 600, Quality score = NCBI/Sanger or Illumina Pipeline 1.8 and later, Remove failed reads = Yes, MiSeq de-multiplexing = No
Sequences were trimmed using: Toolbox -> NGS Core Tools -> Trim Sequences with the following parameters:  Ambigous trim = Yes, Ambiguous limit = 2, Quality trim = Yes, Quality limit = 0,05, Create report = Yes, Save discarded sequences = No, Remove 5'terminal nucleotides = Yes, Number of 5'terminal nucleotides = 3, Minimum number of nucleotides in reads = 50, Dicard short reads = Yes, Remove 3'terminal nucleotides = Yes, Number of 3'terminal nucleotides = 3, Discard long reads = No, Save broken pairs = No
For RPKM calculation, reads were aligned to the Arabidopsis chloroplast genome NC_000932.1 using the RNA-Seq Analysis tool with the following settings: Reference type = Genome annotated with genes only, Reference sequence = NC_000932.1, Gene track = Genome (Gene), Mapping type = Map to gene regions only, Mismatch cost = 2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8, Global alignment = No, Auto-detect paired distances = Yes, Strand specific = Both, Maximum number of hits for a read = 3, Count paired reads as two = No, Expression value = Total counts, Calculate RPKM for genes without transcripts = Yes, Use EM estimation = No, Minimum read count fusion gene table = 5
Resulting RPKM (of chloroplast genes),were exported and the ratio of PUMPKIN vs Pre-immunserum was calculated in Excel
Genome_build: NC_000932.1, Arabidopsis thaliana chloroplast genome

growth_protocol: Plants were grown under controlled conditions (12-h-light (20°C)/12-h-dark (18°C) at a PFD of 100 µmol photons m-2 sec-1)

extract_protocol:
Isolation of chloroplasts and stroma extracts as well as immunprecipitation protocol see: "Meurer, J., Schmid, L.M., Stoppel, R., Leister, D., Brachmann, A., and Manavski, N. (2017). PALE CRESS binds to plastid RNAs and facilitates the biogenesis of the 50S ribosomal subunit. Plant J 92:400-413."
Recovered RNA was used for generation of libraries with the ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre) according to manufacturer's instructions

tag: ecotype

value: wild type

value: 2 weeks

tag: cell type

value: chloroplast; stroma extract

value: PUMPKIN-specific antibodies


title: Dpt rep2

data_processing:
Raw data were imported into CLC Genomics Workbench (Version): File -> Import -> Illumina with the following parameters: Discard quality scores = No, Paired orientation = Paired reads (forward-reverse), Minimum distance = 100, Maximum distance = 600, Quality score = NCBI/Sanger or Illumina Pipeline 1.8 and later, Remove failed reads = Yes, MiSeq de-multiplexing = No
Sequences were trimmed using: Toolbox -> NGS Core Tools -> Trim Sequences with the following parameters:  Ambigous trim = Yes, Ambiguous limit = 2, Quality trim = Yes, Quality limit = 0,05, Create report = Yes, Save discarded sequences = No, Remove 5'terminal nucleotides = Yes, Number of 5'terminal nucleotides = 3, Minimum number of nucleotides in reads = 50, Dicard short reads = Yes, Remove 3'terminal nucleotides = Yes, Number of 3'terminal nucleotides = 3, Discard long reads = No, Save broken pairs = No
Reference genome of Arabidopsis thaliana was imported using: Download -> Download Reference Genome Data -> Genome: Plants: Arabidopsis thaliana -> Download genome sequence; "Sequence" (Version TAIR10, Provider Ensembl Genomes) and "Genome Annotations" (Version TAIR10, Provider Ensembl Genomes) and "Variants"
The downloaded "Arabidopsis thaliana" reference sequence was converted into tracks: Create Track List -> Save the Results
RNA-Seq analysis was perfomed using Toolbox -> Transcriptomics analysis -> RNASeq analysis ->  RNA Seq analysis with following parameters: Reference type = Genome annotated with genes and transcripts, Reference sequence = Arabidopsis thaliana sequence, Gene track = Arabidopsis thaliana_Gene, mRNA track = Arabidopsis thaliana_mRNA, Mapping type = Map to gene regions only, Mismatch cost = 2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8, Global alignment = No, Auto-detect paired distances = Yes, Strand specific = Both, Maximum number of hits for a read = 3, Count paired reads as two = No, Expression value = Total counts, Calculate RPKM for genes without transcripts = Yes, Use EM estimation (recommended) = No, Minimum read count fusion gene table = 5, Create report = Yes, Create fusion gene table = Yes, Create list of unmapped reads = Yes
Resulting RPKM values were filtered for chloroplast genes, exported and the fold change of the two combined replicates was calculated in Excel
Genome_build: Reference genome of Arabidopsis thaliana: Version TAIR10, Provider Ensembl Genomes;
Supplementary_files_format_and_content: Excel File, containing the RPKM values of chloroplast genes of all your samples as well as the fold change calculated for the replicates

source_name: pumpkin mutant_leaf material

growth_protocol: Plants were grown under controlled conditions (12-h-light (20°C)/12-h-dark (18°C) at a PFD of 100 µmol photons m-2 sec-1), age of WT: 3 weeks; age of pumpkin: 6 weeks in order to compare similar developmental stages

extract_protocol:
Total RNA of frozen WT/ pumpkin plants was Trizol-isolated and treated with RiboMinusTM Plant Kit (Thermo)
RNA was subsequently used for generation of libraries with the ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre) according to manufacturer's instructions

tag: ecotype background

value: pumpkin mutant

value: 6 weeks

value: leaves


title: WT rep 1

source_name: WT_leaf material

value: WT

value: 3 weeks


title: ein3eil1+Cd.bam


title: PUMPKIN rep1


title: WT rep 2


title: Dpt rep1


title: A2_NR_I3

value: root

value: interaction with the fungus

value: biological replica 2


title: EUS-FNA_12

city: Tokushima

first: Toshihito

last: Tanahashi

address: Kuramotocho 3-18-5

institute: Tokushima University

description: miRNA expression

hyb_protocol: Cy3-labelled miRNA was hybridized to SurePrint G3 human miRNA microarray (GPL 18402) using miRNA complete labeling reagent and hybridization kit (Agilent).

scan_protocol: Each sample was scanned by a Microarray Scanner (G2505C; Agilent).

data_processing: Fluorescence signal was extracted using Feature Extraction Software (version 10.7.3.1). Raw intensity miRNA data were analyzed by GeneSpring GX 12 (Agilent).

source_name: Adenocarcinoma

label_protocol: Fraction of miRNA was labelled with cyanine 3-cytidine bisphosphate by T4 ligase (Agilent).

extract_protocol: Total RNA including the fraction of miRNA was extracted from EUS-FNA samples and pancreatic cell lines using a miRNeasy Mini Kit (Qiagen). The concentration of RNA was measured with the NanoDrop 1000 spectrophotometer (NanoDrop Technologies), and the quality of the purified RNA was assessed RNA integrity with the Agilent 2100 Bioanalyzer and the RNA 6000 LabChip Kit (Agilent).

treatment_protocol: Thirteen specimens were obtained by endoscopic ultrasound-fine needle aspiration (EUS-FNA) technique with 22- or 25-gauge needle designed for standard cytologic examination and diagnosed as pancreatic ductal adenocarcinoma by the cytopathologist.

value: pancreas

tag: gender

value: Female


title: EUS-FNA_11

description: miRNA expression


title: EUS-FNA_13

description: miRNA expression

value: Male


title: EUS-FNA_08

description: miRNA expression


title: Pre-immune rep2

source_name: Stroma extracts_pre-immune serum

value: pre-immune serum


title: EUS-FNA_07

description: miRNA expression


title: EUS-FNA_05

description: miRNA expression


title: EUS-FNA_06

description: miRNA expression


title: EUS-FNA_10

description: miRNA expression


title: Pa04C: Yap1_S127A

city: HOUSTON

first: HAOQIANG

last: YING

state: TX

address: 1515 Holcombe Blvd

department: Molecular and Cellular Oncology

institute: MD Anderson Cancer Center

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: data are quantile normalized

source_name: Pa04C cell line, constitutive active Yap1

label_protocol: Standard Illumina labelling protocol

growth_protocol: Pa04C cells were maintained in DMEM medium with 10% FBS

extract_protocol: mRNA was extracted with Trizol according to manufacturer's protocol

treatment_protocol: Pa04C cells were transfected with a linearized pcDNA3.1 plasmid with or without YAP1 cDNA containing S127A substitution. Single clones were picked following G418 selection, expanded and injected to nude mice pancreas to establish orthotopic xenograft tumors.


title: EUS-FNA_04

description: miRNA expression


title: EUS-FNA_01

description: miRNA expression


title: EUS-FNA_02

description: miRNA expression


title: EUS-FNA_03

description: miRNA expression


title: H3K27ac_Patient_B_PRAD

city: Amsterdam

first: Wilbert

last: Zwart

address: Plesmanlaan 121

department: Division of Oncogenomics

country: Netherlands

institute: NKI

library_source: genomic

data_processing:
Immunoprecipitated DNA was processed for sequencing using standard protocols and sequenced on an Illumina HiSeq 2500 with 65bp single end reads.
Sequenced samples were aligned to the reference human genome (Ensembl release 55: Homo sapiens GRCh 37.55) using Burrows-Wheeler Aligner (BWA, v0.5.10), reads with a mapping quality > 20 were used for further downstream analysis
For the tissues, peak calling was performed using MACS2 with option --nomodel. In addition, peaks were called against matched input using DFilter in the refine setting with a bandwidth of 50 and a kernel size of 30.
For the cell lines, peaks were obtained with MACS (v1.4; p ≤ 10-7).
The AR and FOXA1 ChIP-seq data for LNCAP with/-out R1881 obtained from GSE94682. The H3K27ac ChIP-seq data for LNCAP was obtained from GSE114737.
BAM files were converted into bedGraph files using deepTools bamCoverage (v3.3.0) using a bin-size of 50 and skipping non-covered positions.
Genome_build: GRCh 37.55
Supplementary_files_format_and_content: BedGraph files from BAM files which contained aligned reads per sample for 7.5Mb up- and downstream of KLK3, TMPRSS2, AR and MYC. BED files contain called MACSMACS2-peaks for the same regions.

source_name: Patient-derived malignant prostate tissue

growth_protocol: fresh frozen material

extract_protocol: Chromatin immunoprecipitations were performed as described previously with minor changes (Zwart et al., 2013). Samples were crosslinked in solution A with 2mM DSG (CovaChem) for 25 minutes at room temperature. After 25 minutes, 1% formaldehyde was added for 20 minutes and subsequently quenched with glycine. Samples were lysed as described (Schmidt et al., 2009) and sonicated for at least 10 cycles of 30s on, 30s off using a Diagenode Bioruptor Pico. For each ChIP, 5ug of antibody was conjugated with 50ul Protein A magnetic beads. Antibodies used were AR (sc-816, Santa Cruz), H3K27ac (39133, Active Motif), H3K4me3 (Ab8580, Abcam) and H3K27me3 (39155, Active Motif). Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).  Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).

treatment_protocol: Surgical resections from prostate tumors.

tag: chip antibody

value: H3K27ac (39133, Active Motif)

value: Prostate

tag: tumor stage

value: Primary prostate adenocarcinoma

tag: strain


title: H3K27ac_Patient_A_PRAD


title: FOXA1_Patient-2_mCRPC

value: Foxa1/2 (M-20, sc-6554 Santa Cruz Biotechnology)


title: FOXA1_Patient_B_PRAD


title: FOXA1_Patient-1_mCRPC


title: FOXA1_Patient_C_PRAD


title: H3K27ac_Patient_C_PRAD


title: H3K27ac_Patient-2_mCRPC


title: H3K27ac_Patient-1_mCRPC


title: EUS-FNA_09

description: miRNA expression

tag: age


title: AR_Patient_C_PRAD

value: AR (N-20, sc-816 Santa Cruz Biotechnology)


title: AR_Patient_B_PRAD


title: FOXA1_Patient_A_PRAD


title: AR_VCaP-Bicalutamide

source_name: Prostate cancer cell line

value: VCaP


title: AR_Patient_A_PRAD


title: AR_Patient-2_mCRPC

value: Castration-resistant metastatis


title: AR_VCaP


title: Pa04C: vector

description: replicate 1

source_name: Pa04C cell line, vector control


title: AR_Patient-1_mCRPC


title: KIF4

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

value: iPS cells


title: KIF4(H2O2_ 3hr)

description: KIF4(H2O2_ 3hr)

source_name: KIF4(H2O2_ 3hr)

tag: agent

tag: time point


title: KIF4(H2O2_ 6hr)

description: KIF4(H2O2_ 6hr)

source_name: KIF4(H2O2_ 6hr)


title: fibroblast(H2O2_6h)

value: fibroblast cells


title: fibroblast(H2O2_24h)


title: fibroblast(H2O2_3h)


title: HLA chr6 No1

description: hiPSC-telHLAcNP/+ML216(+)HLA I-III-CRISPR(+) No1--2


title: HLA chr6 No1(Rock inh.)

description: hiPSC-telHLAcNP/+ML216(+)HLA I-III-CRISPR(+) No1-4


title: HLA chr6 No1 control

description: hiPSC-telHLAcNP/+ML216(+)HLA I-III-CRISPR(+) No1--3


title: Pre-immune rep1

value: wild type

value: 2 weeks

value: chloroplast; stroma extract


title: fibroblast(control)

description: Fibroblast cells

source_name: Fibroblast cells


title: HLA chr6(No2) p2

description: hiPSC-telHLAcNP/+ML216(+)HLA I-III-CRISPR(+) No2-1


title: HLA chr6(No1) p2

description: hiPSC-telHLAcNP/+ML216(+)HLA I-III-CRISPR(+) No1-11


title: HLA chr6(No1) p3

description: hiPSC-telHLAcNP/+ML216(+)HLA I-III-CRISPR(+) No1-5


title: Patient31

city: Dallas

first: W. Lee

last: Kraus

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
The RNA-seq reads were aligned to the hg19 human reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and  bigwig files were generated to for presentation as browser tracks using BedGraph and BigWig function of UCSC tool kit.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

source_name: Tumor specimens of patients with high-grade serous ovarian cancer

growth_protocol: Tissue samples were obtained intra-operatively from surgical tumor specimens of patients with high-grade serous ovarian cancer at the time of the planned cytoreductive surgery under a tissue repository protocol from 2009 to 2014.

extract_protocol: Total RNA was isolated from each ovarian cancer tissue sample using an RNeasy Plus Kit (Qiagen), with QIAshredder spin columns for homogenization and on-column DNaseI digestion (79254, Qiagen).  The total RNA was analyzed for integrity using an Agilent 2100 Bioanalyzer.  The RNA collected was then processed for whole-genome polyadenylated RNA sequencing (polyA+ RNA-seq). The total RNA samples were enriched for polyA+ RNA using Dynabead Oligo(dT)25 (Invitrogen) and strand-specific RNA-seq libraries were prepared from the polyA+ RNA as described previously.  The RNA-seq libraries were sequenced using an Illumina HiSeq 2500 (single-end, 50 nt; SE50; one replicate).

tag: patient diagnosis

value: high-grade serous ovarian cancer

tag: tissue

value: ovarian tumor


title: Patient28


title: Patient34


title: Patient30


title: Patient26


title: Patient29


title: Patient25


title: Patient23


title: Patient12


title: Patient9


title: Patient18


title: Patient17


title: Patient7


title: Patient21


title: SPI21.2

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

description:
batch2
cellular labeled RNA

data_processing:
Library strategy: 4sU-seq
Sequences were analysed using the RNA-Seq pipeline of UTAP  (Kohen et al. BMC Bioinformatics (2019) 20:154 https://doi.org/10.1186/s12859-019-2728-2) with batch correction.
In this pipeline the reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200) and mapped to genome hg38 using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (default parameters).
The pipeline quantifies the genes annotated in RefSeq (downloaded from iGenomes).
Gene expression counting was done using STAR.
Further analysis is done for genes having minimum 5 read in at least one sample.
Normalization of the counts and differential expression analysis was performed using DESeq2 (DOI: 10.1186/s13059-014-0550-8) with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. In the contrast DMSO_TNF_vs_DMSO and SPI21_TNF_vs_SPI21 fdrtools was applied. Batch corrected normalized log2 counts are termed combat values and were calculated using “sva” package of R
The thresholds for significant differential expression (DE) are: padj <= 0.05 & |log2FoldChange| >= 1 & baseMean >= 5
Genome_build: hg38
Supplementary_files_format_and_content: Excel

source_name: HeLa cells

growth_protocol: HeLa cells were grown and maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal calf serum (Gibco) and 1% penicillin-streptomycin. To avoid basal NF-кB activity, HeLa cells were kept from reaching confluence and re-plated after initial thawing no more than 10 times.

extract_protocol:
4sU-labeled RNA was biotinylated, purified and captured using Streptavidin-coated magnetic beads.
4sU-seq RNA samples were reverse transcribed using inhouse mRNA Seq protocol w/o PolyA capture with random hexamers.

treatment_protocol: HeLa cells were metabolically labeled with 4-thio-uridine (4sU) for 2 hours in the presence of DMSO or SPI-21 and in the presence or absence of TNFα.

tag: cell line

value: HeLa cells


title: SPI21.1

description:
batch1
cellular labeled RNA


title: Patient8


title: Patient5


title: DMSO.2

description:
batch2
cellular labeled RNA

value: DMSO


title: KIF4(H2O2_24h)


title: SPI21_TNF2

description:
batch2
cellular labeled RNA

value: SPI21 + TNF


title: Patient13


title: Patient2


title: DMSO.1

description:
batch1
cellular labeled RNA


title: SPI21_1_GRO-seq

data_processing:
Library strategy: GRO-seq
GRO-seq were analysed using the RNA-Seq pipeline of UTAP  (Kohen et al. BMC Bioinformatics (2019) 20:154 https://doi.org/10.1186/s12859-019-2728-2).
In this pipeline the reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200) and mapped to genome hg38 using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (default parameters).
The pipeline quantifies the genes annotated in RefSeq (downloaded from iGenomes).
Gene expression counting was done using STAR.
Pausing index (PI) analysis was done for the genes that had at least 50 reads in any of the DMSO samples. Symbol  and transcript average length per gene and raw counts per gene were merged using a dedicated R script.
First the reads coverage was calculated using bed files containing the desired genomic regions and orientation (awk command) and the bedtools coverage tool (Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842). Latter this information was merged with the transcript accession , gene symbol  and transcript average length per gene using a dedicated R script.  PI was calculated by dividing Pol II density (reads/1000bp) around the TSS (-300 to +700 bp) by Pol II density in the gene body (+700 to +1700).
Genome_build: hg38
Supplementary_files_format_and_content: Excel with PI calculations and raw gene counts

molecule: nuclear RNA

extract_protocol:
Nuclei were isolated from pre-treted HeLa cells using 27G needle in lysis buffer. Nuclear Run-on was proceed for 5 min in the presence of Sarkosyl and Br-UTP. RNA was extracted and fragmented and then BrU-labeled RNA was purified with anti-BrdU beads.
GRO-seq RNA samples were reverse transcribed and amplified (15 cycles) using inhouse mRNA Seq protocol w/o PolyA capture with random hexamers.

treatment_protocol: HeLa cells pre-treated with either DMSO (control) or SPI-21 (50μM) for 1.5 hours


title: SPI21_2+TNF_24h

data_processing:
Sequences were analysed using the RNA-Seq pipeline of UTAP  (Kohen et al. BMC Bioinformatics (2019) 20:154 https://doi.org/10.1186/s12859-019-2728-2).
In this pipeline the reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200) and mapped to genome hg38 using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (default parameters).
The pipeline quantifies the genes annotated in RefSeq (downloaded from iGenomes).
Gene expression counting was done using STAR.
Further analysis is done for genes having minimum 5 read in at least one sample.
Normalization of the counts and differential expression analysis was performed using DESeq2 (DOI: 10.1186/s13059-014-0550-8) with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. In the contrast DMSO24_vs_DMSO_T24 and SPI21_24_vs_SPI21_T_24 fdrtools was applied.  Batch corrected normalized log2 values expression values were extracted using combat from svn package in R .
The thresholds for significant differential expression (DE) are: padj <= 0.05 & |log2FoldChange| >= 1 & baseMean >= 5
Genome_build: hg38
Supplementary_files_format_and_content: Excel

extract_protocol:
Total RNA was extracted and subjected to RNA-seq.
Total RNA samples were reverse transcribed using inhouse mRNA Seq protocol w/o PolyA capturing using random hexamers.

treatment_protocol: HeLa cells were treated for 24 hours in the presence of DMSO or SPI-21 and in the presence or absence of TNFα.

value: SPI21+TNF 24h


title: DMSO_2_GRO-seq


title: SPI21_2_24h

value: SPI21 24h


title: DMSO_TNF1

description:
batch1
cellular labeled RNA

value: DMS + TNF


title: Patient11


title: Patient6


title: Patient22


title: SPI21_TNF1

description:
batch1
cellular labeled RNA


title: SPI21_1_24h


title: DMSO+TNF_2_24h

value: DMSO+TNF 24h


title: DMSO+TNF_1_24h


title: DMSO_TNF2

description:
batch2
cellular labeled RNA


title: SPI21_2_2h

data_processing:
Illumina bcl2fastq2.17 was used for basecalling.
Sequenced reads were trimmed from adaptor sequence, polyA/T sequences and low quality bases (quality score <10) at the beginning and end of all reads using cutadapt1.10. reads shorter than 30bp were discarded.
Mapping to GRCh38 genome was done using STAR v.2.4.2a with overhang set to 60 in  'EndToEnd' mode, supplied with Ensembel's annotation v.88
Couting was done using Htseq on exons in intersection-strict mode
Counts normalization and differential expression was carried out with DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: text files containing raw counts (CountsMatrix.tsv) and normalized counts per gene (countsMatrix_normalized.csv)

extract_protocol:
Total RNA was extracted and subjected to RNA-seq.
Total RNA samples were reverse transcribed using inhouse mRNA Seq protocol with PolyA capturing.

treatment_protocol: HeLa cells were treated for 2 hours in the presence of DMSO or SPI-21 and in the presence or absence of TNFα.

value: SPI21 2h


title: SPI21_2+TNF_2h

value: SPI21+TNF 2h


title: DMSO_2_24h

value: DMSO 24h


title: DMSO_1_GRO-seq


title: DMSO_2_2h

value: DMSO 2h


title: DMSO_1_2h


title: Liver tissue, Infection, 932_08L

description: Tissue from liver

source_name: Liver tissue

tag: condition

value: Infection

value: Liver

value: 112 weeks

value: male


title: DMSO+TNF_1_2h

tag: treatment

value: DMSO+TNF 2h


title: SPI21_1+TNF_24h


title: SPI21_1_2h


title: Per_R9_C22

city: Houston

first: Qingnan

last: Liang

address: One Baylor Plaza

department: HGSC

institute: Baylor College of Medicine

description: P3_Per.txt (matrix)

data_processing:
Illumina Casava software used for basecalling. Individual FASTQ files obtained were demultiplexed using the well-specific barcode identifiers for downstream data processing and analysis.
FASTQ sequences were mapped to human genome hg19 (GRCh37) downloaded from UCSC genome browser website and aligned using TopHat2
Transcript structure and abundance were estimated using HTseq and Cufflink
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: retina

extract_protocol:
Single nuclear capture and sequencing were performed on the ICELL8 single cell platform (Wafergen Biosytems). ICELL8 platform comprised of a multi-sample nano-dispenser that precisely dispensed 50nl of the single nuclei suspension into an ICELL8 nanowell microchip-containing 5184 wells (150nl capacity). Assuming a Poisson distribution frequency for the number of cells per well, about 30% of the nanowells were expected to contain a single nucleus under optimal conditions. Automated scanning fluorescent microscopy of the microchip was performed using an Olympus BX43 fluorescent microscope with a robotic stage to visualize wells containing single nuclei (see Table 1 for single cell capture number across different experimental repeats). The automated well selection was performed using the CellSelect software (Wafergen Biosystems), which identified nanowells containing single nuclei and excluded wells with >1 nuclear, debris, nuclei clumps or empty wells. The candidate wells were manually evaluated for debris or clumps as an additional QC.
The chip was subjected to freeze-thaw in order to lyse the cells and 50 nl of reverse transcription and amplification solution (following ICELL8 protocol) was dispensed using the multi-sample nano-dispenser to candidate wells. Each well had a preprinted primer that contains an 11-nucleotide-well-specific barcode. This barcode was added to the 3’ (A)n RNA tail of the nuclear transcripts during reverse transcription and cDNA amplification, the latter of which was performed on candidate wells using SCRB-seq chemistry. After RT, the cDNA products from candidate wells were pooled, concentrated (Zymo Clean and Concentrator kit, Zymogen) and purified using 0.6x AMPure XP beads. A 3’ transcriptome enriched library was made using Nextera XT Kit and 3’-specific P5 primer, which was sequenced on the Illumina Hiseq2500.

treatment_protocol: Nuclei from frozen neural retinal tissue was isolated using RNase-free lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl¬2, 0.1% NP40). The frozen tissue was resuspended in ice-cold lysis buffer and triturated to break the tissue structure. The tissue aggregates were then homogenized using a Wheaton™ Dounce Tissue Grinder and centrifuged (500g) to pellet the nuclei. The pellet was re-suspended in fresh lysis buffer and homogenized to yield clean single-nuclei suspension. The collected nuclei were stained with DAPI (4',6-diamidino-2-phenylindole, 10ug/ml) and were diluted to 1000 μl of 3E4/ml with 1× PBS (without Ca and Mg ions, pH 7.4, Thermo Fisher), RNase inhibitor (NEB, 40KU/ml) and Cell Diluent Buffer.

tag: sample

value: Retina


title: Per_R9_C18

description: P3_Per.txt (matrix)


title: Per_R9_C46

description: P3_Per.txt (matrix)


title: Per_R9_C67

description: P3_Per.txt (matrix)


title: Per_R8_C62

description: P3_Per.txt (matrix)


title: Per_R8_C64

description: P3_Per.txt (matrix)


title: Patient4

value: high-grade serous ovarian cancer

value: ovarian tumor


title: Per_R8_C67

description: P3_Per.txt (matrix)


title: Per_R8_C61

description: P3_Per.txt (matrix)


title: DMSO_1_24h

value: HeLa cells


title: Per_R8_C42

description: P3_Per.txt (matrix)


title: Per_R8_C41

description: P3_Per.txt (matrix)


title: DMSO+TNF_2_2h


title: SPI21_1+TNF_2h


title: Per_R8_C18

description: P3_Per.txt (matrix)


title: Per_R8_C20

description: P3_Per.txt (matrix)


title: Per_R8_C37

description: P3_Per.txt (matrix)


title: Per_R9_C63

description: P3_Per.txt (matrix)


title: Per_R8_C17

description: P3_Per.txt (matrix)


title: Per_R7_C63

description: P3_Per.txt (matrix)


title: Per_R7_C37

description: P3_Per.txt (matrix)


title: Per_R7_C42

description: P3_Per.txt (matrix)


title: Per_R7_C13

description: P3_Per.txt (matrix)


title: Per_R9_C15

description: P3_Per.txt (matrix)


title: Per_R71_C60

description: P3_Per.txt (matrix)


title: Per_R7_C60

description: P3_Per.txt (matrix)


title: Per_R71_C47

description: P3_Per.txt (matrix)


title: Per_R71_C64

description: P3_Per.txt (matrix)


title: Per_R71_C45

description: P3_Per.txt (matrix)


title: Per_R71_C23

description: P3_Per.txt (matrix)


title: Per_R71_C43

description: P3_Per.txt (matrix)


title: Per_R70_C71

description: P3_Per.txt (matrix)


title: Per_R70_C45

description: P3_Per.txt (matrix)


title: Per_R71_C38

description: P3_Per.txt (matrix)


title: Per_R71_C17

description: P3_Per.txt (matrix)


title: Per_R7_C70

description: P3_Per.txt (matrix)


title: Per_R70_C62

description: P3_Per.txt (matrix)


title: Per_R70_C37

description: P3_Per.txt (matrix)


title: Per_R70_C38

description: P3_Per.txt (matrix)


title: Per_R6_C64

description: P3_Per.txt (matrix)


title: Per_R70_C13

description: P3_Per.txt (matrix)


title: Per_R6_C65

description: P3_Per.txt (matrix)


title: Per_R70_C16

description: P3_Per.txt (matrix)


title: Per_R6_C47

description: P3_Per.txt (matrix)


title: Per_R6_C44

description: P3_Per.txt (matrix)


title: Per_R6_C45

description: P3_Per.txt (matrix)


title: Per_R6_C42

description: P3_Per.txt (matrix)


title: Per_R6_C22

description: P3_Per.txt (matrix)


title: Per_R69_C70

description: P3_Per.txt (matrix)


title: Per_R6_C46

description: P3_Per.txt (matrix)


title: Per_R69_C64

description: P3_Per.txt (matrix)


title: Per_R69_C66

description: P3_Per.txt (matrix)


title: Per_R6_C37

description: P3_Per.txt (matrix)


title: Per_R6_C41

description: P3_Per.txt (matrix)


title: Per_R6_C15

description: P3_Per.txt (matrix)


title: Per_R71_C12

description: P3_Per.txt (matrix)


title: Per_R69_C63

description: P3_Per.txt (matrix)


title: Per_R69_C62

description: P3_Per.txt (matrix)


title: Per_R69_C61

description: P3_Per.txt (matrix)


title: Per_R69_C44

description: P3_Per.txt (matrix)


title: Per_R69_C45

description: P3_Per.txt (matrix)


title: Per_R69_C43

description: P3_Per.txt (matrix)


title: Per_R69_C38

description: P3_Per.txt (matrix)


title: Per_R8_C44

description: P3_Per.txt (matrix)


title: Per_R69_C36

description: P3_Per.txt (matrix)


title: Per_R69_C23

description: P3_Per.txt (matrix)


title: Per_R69_C18

description: P3_Per.txt (matrix)


title: Per_R68_C70

description: P3_Per.txt (matrix)


title: Per_R68_C65

description: P3_Per.txt (matrix)


title: Per_R68_C63

description: P3_Per.txt (matrix)


title: Per_R68_C44

description: P3_Per.txt (matrix)


title: Per_R68_C42

description: P3_Per.txt (matrix)


title: Per_R71_C14

description: P3_Per.txt (matrix)


title: Per_R68_C64

description: P3_Per.txt (matrix)


title: Per_R68_C15

description: P3_Per.txt (matrix)


title: Per_R68_C17

description: P3_Per.txt (matrix)


title: Per_R68_C19

description: P3_Per.txt (matrix)


title: Per_R68_C23

description: P3_Per.txt (matrix)


title: Per_R67_C68

description: P3_Per.txt (matrix)


title: Per_R67_C22

description: P3_Per.txt (matrix)


title: Per_R67_C63

description: P3_Per.txt (matrix)


title: Per_R67_C23

description: P3_Per.txt (matrix)


title: Per_R67_C39

description: P3_Per.txt (matrix)


title: Per_R67_C13

description: P3_Per.txt (matrix)


title: Per_R66_C68

description: P3_Per.txt (matrix)


title: Per_R68_C67

description: P3_Per.txt (matrix)


title: Per_R66_C23

description: P3_Per.txt (matrix)


title: Per_R66_C64

description: P3_Per.txt (matrix)


title: Per_R66_C36

description: P3_Per.txt (matrix)


title: Per_R66_C39

description: P3_Per.txt (matrix)


title: Per_R65_C66

description: P3_Per.txt (matrix)


title: Per_R66_C61

description: P3_Per.txt (matrix)


title: Per_R67_C67

description: P3_Per.txt (matrix)


title: Per_R66_C43

description: P3_Per.txt (matrix)


title: Per_R66_C37

description: P3_Per.txt (matrix)


title: Per_R65_C39

description: P3_Per.txt (matrix)


title: Per_R65_C69

description: P3_Per.txt (matrix)


title: Per_R65_C19

description: P3_Per.txt (matrix)


title: Per_R65_C17

description: P3_Per.txt (matrix)


title: Per_R65_C22

description: P3_Per.txt (matrix)


title: Per_R65_C14

description: P3_Per.txt (matrix)


title: Per_R67_C19

description: P3_Per.txt (matrix)


title: Per_R64_C63

description: P3_Per.txt (matrix)


title: Per_R64_C67

description: P3_Per.txt (matrix)


title: Per_R64_C47

description: P3_Per.txt (matrix)


title: Per_R66_C65

description: P3_Per.txt (matrix)


title: Per_R66_C70

description: P3_Per.txt (matrix)


title: Per_R64_C43

description: P3_Per.txt (matrix)


title: Per_R64_C42

description: P3_Per.txt (matrix)


title: Per_R64_C45

description: P3_Per.txt (matrix)


title: Per_R64_C40

description: P3_Per.txt (matrix)


title: Per_R64_C38

description: P3_Per.txt (matrix)


title: Per_R64_C23

description: P3_Per.txt (matrix)


title: Per_R65_C12

description: P3_Per.txt (matrix)


title: Per_R65_C16

description: P3_Per.txt (matrix)


title: Per_R64_C20

description: P3_Per.txt (matrix)


title: Per_R64_C19

description: P3_Per.txt (matrix)


title: Per_R63_C71

description: P3_Per.txt (matrix)


title: Per_R63_C69

description: P3_Per.txt (matrix)


title: Per_R63_C65

description: P3_Per.txt (matrix)


title: Per_R63_C61

description: P3_Per.txt (matrix)


title: Per_R63_C63

description: P3_Per.txt (matrix)


title: Per_R63_C47

description: P3_Per.txt (matrix)


title: Per_R63_C68

description: P3_Per.txt (matrix)


title: Per_R63_C60

description: P3_Per.txt (matrix)


title: Per_R63_C45

description: P3_Per.txt (matrix)


title: Per_R62_C69

description: P3_Per.txt (matrix)


title: Per_R63_C20

description: P3_Per.txt (matrix)


title: Per_R63_C17

description: P3_Per.txt (matrix)


title: Per_R63_C12

description: P3_Per.txt (matrix)


title: Per_R63_C21

description: P3_Per.txt (matrix)


title: Per_R63_C41

description: P3_Per.txt (matrix)


title: Per_R63_C18

description: P3_Per.txt (matrix)


title: Per_R62_C67

description: P3_Per.txt (matrix)


title: Per_R62_C46

description: P3_Per.txt (matrix)


title: Per_R62_C63

description: P3_Per.txt (matrix)


title: Per_R62_C60

description: P3_Per.txt (matrix)


title: Per_R62_C44

description: P3_Per.txt (matrix)


title: Per_R62_C42

description: P3_Per.txt (matrix)


title: Per_R62_C64

description: P3_Per.txt (matrix)


title: Per_R62_C37

description: P3_Per.txt (matrix)


title: Per_R63_C36

description: P3_Per.txt (matrix)


title: Per_R63_C44

description: P3_Per.txt (matrix)


title: Per_R62_C22

description: P3_Per.txt (matrix)


title: Per_R61_C69

description: P3_Per.txt (matrix)


title: Per_R61_C71

description: P3_Per.txt (matrix)


title: Per_R61_C68

description: P3_Per.txt (matrix)


title: Per_R61_C61

description: P3_Per.txt (matrix)


title: Per_R62_C19

description: P3_Per.txt (matrix)


title: Per_R61_C14

description: P3_Per.txt (matrix)


title: Per_R67_C20

description: P3_Per.txt (matrix)


title: Per_R61_C19

description: P3_Per.txt (matrix)


title: Per_R61_C12

description: P3_Per.txt (matrix)


title: Per_R61_C38

description: P3_Per.txt (matrix)


title: Per_R60_C71

description: P3_Per.txt (matrix)


title: Per_R60_C68

description: P3_Per.txt (matrix)


title: Per_R60_C43

description: P3_Per.txt (matrix)


title: Per_R60_C64

description: P3_Per.txt (matrix)


title: Per_R60_C42

description: P3_Per.txt (matrix)


title: Per_R60_C65

description: P3_Per.txt (matrix)


title: Per_R60_C39

description: P3_Per.txt (matrix)


title: Per_R60_C20

description: P3_Per.txt (matrix)


title: Per_R60_C19

description: P3_Per.txt (matrix)


title: Per_R60_C14

description: P3_Per.txt (matrix)


title: Per_R60_C17

description: P3_Per.txt (matrix)


title: Per_R5_C69

description: P3_Per.txt (matrix)


title: Per_R60_C18

description: P3_Per.txt (matrix)


title: Per_R5_C61

description: P3_Per.txt (matrix)


title: Per_R5_C60

description: P3_Per.txt (matrix)


title: Per_R61_C23

description: P3_Per.txt (matrix)


title: Per_R5_C45

description: P3_Per.txt (matrix)


title: Per_R5_C39

description: P3_Per.txt (matrix)


title: Per_R61_C63

description: P3_Per.txt (matrix)


title: Per_R5_C23

description: P3_Per.txt (matrix)


title: Per_R5_C41

description: P3_Per.txt (matrix)


title: Per_R5_C42

description: P3_Per.txt (matrix)


title: Per_R5_C40

description: P3_Per.txt (matrix)


title: Per_R59_C67

description: P3_Per.txt (matrix)


title: Per_R5_C19

description: P3_Per.txt (matrix)


title: Per_R5_C17

description: P3_Per.txt (matrix)


title: Per_R59_C62

description: P3_Per.txt (matrix)


title: Per_R59_C47

description: P3_Per.txt (matrix)


title: Per_R59_C65

description: P3_Per.txt (matrix)


title: Per_R59_C46

description: P3_Per.txt (matrix)


title: Per_R60_C67

description: P3_Per.txt (matrix)


title: Per_R59_C43

description: P3_Per.txt (matrix)


title: Per_R59_C44

description: P3_Per.txt (matrix)


title: Per_R59_C37

description: P3_Per.txt (matrix)


title: Per_R59_C22

description: P3_Per.txt (matrix)


title: Per_R59_C21

description: P3_Per.txt (matrix)


title: Per_R59_C36

description: P3_Per.txt (matrix)


title: Per_R59_C17

description: P3_Per.txt (matrix)


title: Per_R59_C15

description: P3_Per.txt (matrix)


title: Per_R59_C40

description: P3_Per.txt (matrix)


title: Per_R59_C14

description: P3_Per.txt (matrix)


title: Per_R58_C71

description: P3_Per.txt (matrix)


title: Per_R59_C19

description: P3_Per.txt (matrix)


title: Per_R58_C70

description: P3_Per.txt (matrix)


title: Per_R58_C19

description: P3_Per.txt (matrix)


title: Per_R58_C17

description: P3_Per.txt (matrix)


title: Per_R58_C65

description: P3_Per.txt (matrix)


title: Per_R58_C12

description: P3_Per.txt (matrix)


title: Per_R58_C63

description: P3_Per.txt (matrix)


title: Per_R58_C66

description: P3_Per.txt (matrix)


title: Per_R57_C71

description: P3_Per.txt (matrix)


title: Per_R57_C65

description: P3_Per.txt (matrix)


title: Per_R57_C69

description: P3_Per.txt (matrix)


title: Per_R57_C64

description: P3_Per.txt (matrix)


title: Per_R57_C68

description: P3_Per.txt (matrix)


title: Per_R57_C21

description: P3_Per.txt (matrix)


title: Per_R57_C45

description: P3_Per.txt (matrix)


title: Per_R57_C46

description: P3_Per.txt (matrix)


title: Per_R57_C19

description: P3_Per.txt (matrix)


title: Per_R57_C41

description: P3_Per.txt (matrix)


title: Per_R57_C23

description: P3_Per.txt (matrix)


title: Per_R59_C12

description: P3_Per.txt (matrix)


title: Per_R57_C18

description: P3_Per.txt (matrix)


title: Per_R56_C67

description: P3_Per.txt (matrix)


title: Per_R57_C15

description: P3_Per.txt (matrix)


title: Per_R57_C16

description: P3_Per.txt (matrix)


title: Per_R56_C64

description: P3_Per.txt (matrix)


title: Per_R56_C65

description: P3_Per.txt (matrix)


title: Per_R56_C47

description: P3_Per.txt (matrix)


title: Per_R56_C43

description: P3_Per.txt (matrix)


title: Per_R58_C15

description: P3_Per.txt (matrix)


title: Per_R56_C18

description: P3_Per.txt (matrix)


title: Per_R56_C21

description: P3_Per.txt (matrix)


title: Per_R56_C37

description: P3_Per.txt (matrix)


title: Per_R56_C19

description: P3_Per.txt (matrix)


title: Per_R55_C68

description: P3_Per.txt (matrix)


title: Per_R55_C69

description: P3_Per.txt (matrix)


title: Per_R56_C14

description: P3_Per.txt (matrix)


title: Per_R56_C71

description: P3_Per.txt (matrix)


title: Per_R55_C40

description: P3_Per.txt (matrix)


title: Per_R55_C23

description: P3_Per.txt (matrix)


title: Per_R55_C36

description: P3_Per.txt (matrix)


title: Per_R55_C19

description: P3_Per.txt (matrix)


title: Per_R55_C47

description: P3_Per.txt (matrix)


title: Per_R55_C41

description: P3_Per.txt (matrix)


title: Per_R54_C63

description: P3_Per.txt (matrix)


title: Per_R54_C60

description: P3_Per.txt (matrix)


title: Per_R55_C12

description: P3_Per.txt (matrix)


title: Per_R55_C44

description: P3_Per.txt (matrix)


title: Per_R54_C61

description: P3_Per.txt (matrix)


title: Per_R54_C20

description: P3_Per.txt (matrix)


title: Per_R54_C46

description: P3_Per.txt (matrix)


title: Per_R54_C39

description: P3_Per.txt (matrix)


title: Per_R54_C65

description: P3_Per.txt (matrix)


title: Per_R54_C18

description: P3_Per.txt (matrix)


title: Per_R54_C17

description: P3_Per.txt (matrix)


title: Per_R54_C23

description: P3_Per.txt (matrix)


title: Per_R54_C15

description: P3_Per.txt (matrix)


title: Per_R53_C67

description: P3_Per.txt (matrix)


title: Per_R54_C14

description: P3_Per.txt (matrix)


title: Per_R54_C13

description: P3_Per.txt (matrix)


title: Per_R55_C62

description: P3_Per.txt (matrix)


title: Per_R53_C43

description: P3_Per.txt (matrix)


title: Per_R53_C63

description: P3_Per.txt (matrix)


title: Per_R53_C44

description: P3_Per.txt (matrix)


title: Per_R53_C45

description: P3_Per.txt (matrix)


title: Per_R53_C41

description: P3_Per.txt (matrix)


title: Per_R53_C13

description: P3_Per.txt (matrix)


title: Per_R53_C12

description: P3_Per.txt (matrix)


title: Per_R52_C45

description: P3_Per.txt (matrix)


title: Per_R56_C36

description: P3_Per.txt (matrix)


title: Per_R52_C62

description: P3_Per.txt (matrix)


title: Per_R54_C43

description: P3_Per.txt (matrix)


title: Per_R52_C18

description: P3_Per.txt (matrix)


title: Per_R52_C60

description: P3_Per.txt (matrix)


title: Per_R52_C46

description: P3_Per.txt (matrix)


title: Per_R52_C70

description: P3_Per.txt (matrix)


title: Per_R52_C13

description: P3_Per.txt (matrix)


title: Per_R52_C17

description: P3_Per.txt (matrix)


title: Per_R52_C47

description: P3_Per.txt (matrix)


title: Per_R51_C62

description: P3_Per.txt (matrix)


title: Per_R52_C19

description: P3_Per.txt (matrix)


title: Per_R51_C68

description: P3_Per.txt (matrix)


title: Per_R52_C61

description: P3_Per.txt (matrix)


title: Per_R51_C22

description: P3_Per.txt (matrix)


title: Per_R51_C66

description: P3_Per.txt (matrix)


title: Per_R51_C17

description: P3_Per.txt (matrix)


title: Per_R51_C15

description: P3_Per.txt (matrix)


title: Per_R51_C16

description: P3_Per.txt (matrix)


title: Per_R51_C46

description: P3_Per.txt (matrix)


title: Per_R51_C64

description: P3_Per.txt (matrix)


title: Per_R51_C21

description: P3_Per.txt (matrix)


title: Per_R51_C43

description: P3_Per.txt (matrix)


title: Per_R51_C13

description: P3_Per.txt (matrix)


title: Per_R51_C67

description: P3_Per.txt (matrix)


title: Per_R50_C68

description: P3_Per.txt (matrix)


title: Per_R50_C64

description: P3_Per.txt (matrix)


title: Per_R50_C66

description: P3_Per.txt (matrix)


title: Per_R4_C68

description: P3_Per.txt (matrix)


title: Per_R4_C61

description: P3_Per.txt (matrix)


title: Per_R4_C44

description: P3_Per.txt (matrix)


title: Per_R51_C61

description: P3_Per.txt (matrix)


title: Per_R50_C22

description: P3_Per.txt (matrix)


title: Per_R4_C36

description: P3_Per.txt (matrix)


title: Per_R4_C20

description: P3_Per.txt (matrix)


title: Per_R4_C37

description: P3_Per.txt (matrix)


title: Per_R4_C19

description: P3_Per.txt (matrix)


title: Per_R4_C43

description: P3_Per.txt (matrix)


title: Per_R4_C13

description: P3_Per.txt (matrix)


title: Per_R4_C22

description: P3_Per.txt (matrix)


title: Per_R49_C70

description: P3_Per.txt (matrix)


title: Per_R49_C60

description: P3_Per.txt (matrix)


title: Per_R49_C44

description: P3_Per.txt (matrix)


title: Per_R4_C12

description: P3_Per.txt (matrix)


title: Per_R49_C42

description: P3_Per.txt (matrix)


title: Per_R49_C19

description: P3_Per.txt (matrix)


title: Per_R53_C40

description: P3_Per.txt (matrix)


title: Per_R49_C16

description: P3_Per.txt (matrix)


title: Per_R48_C66

description: P3_Per.txt (matrix)


title: Per_R50_C67

description: P3_Per.txt (matrix)


title: Per_R48_C44

description: P3_Per.txt (matrix)


title: Per_R50_C61

description: P3_Per.txt (matrix)


title: Per_R48_C16

description: P3_Per.txt (matrix)


title: Per_R50_C13

description: P3_Per.txt (matrix)


title: Per_R48_C41

description: P3_Per.txt (matrix)


title: Per_R48_C14

description: P3_Per.txt (matrix)


title: Per_R47_C65

description: P3_Per.txt (matrix)


title: Per_R48_C13

description: P3_Per.txt (matrix)


title: Per_R47_C40

description: P3_Per.txt (matrix)


title: Per_R47_C62

description: P3_Per.txt (matrix)


title: Per_R47_C22

description: P3_Per.txt (matrix)


title: Per_R47_C37

description: P3_Per.txt (matrix)


title: Per_R47_C69

description: P3_Per.txt (matrix)


title: Per_R47_C71

description: P3_Per.txt (matrix)


title: Per_R47_C17

description: P3_Per.txt (matrix)


title: Per_R47_C15

description: P3_Per.txt (matrix)


title: Per_R46_C70

description: P3_Per.txt (matrix)


title: Per_R48_C18

description: P3_Per.txt (matrix)


title: Per_R46_C69

description: P3_Per.txt (matrix)


title: Per_R48_C22

description: P3_Per.txt (matrix)


title: Per_R48_C69

description: P3_Per.txt (matrix)


title: Per_R46_C62

description: P3_Per.txt (matrix)


title: Per_R46_C45

description: P3_Per.txt (matrix)


title: Per_R47_C64

description: P3_Per.txt (matrix)


title: Per_R46_C41

description: P3_Per.txt (matrix)


title: Per_R46_C22

description: P3_Per.txt (matrix)


title: Per_R45_C65

description: P3_Per.txt (matrix)


title: Per_R45_C66

description: P3_Per.txt (matrix)


title: Per_R45_C64

description: P3_Per.txt (matrix)


title: Per_R46_C12

description: P3_Per.txt (matrix)


title: Per_R45_C46

description: P3_Per.txt (matrix)


title: Per_R46_C23

description: P3_Per.txt (matrix)


title: Per_R47_C20

description: P3_Per.txt (matrix)


title: Per_R46_C20

description: P3_Per.txt (matrix)


title: Per_R44_C64

description: P3_Per.txt (matrix)


title: Per_R45_C19

description: P3_Per.txt (matrix)


title: Per_R45_C43

description: P3_Per.txt (matrix)


title: Per_R45_C38

description: P3_Per.txt (matrix)


title: Per_R46_C63

description: P3_Per.txt (matrix)


title: Per_R46_C60

description: P3_Per.txt (matrix)


title: Per_R47_C14

description: P3_Per.txt (matrix)


title: Per_R45_C37

description: P3_Per.txt (matrix)


title: Per_R45_C40

description: P3_Per.txt (matrix)


title: Per_R44_C62

description: P3_Per.txt (matrix)


title: Per_R46_C61

description: P3_Per.txt (matrix)


title: Per_R44_C63

description: P3_Per.txt (matrix)


title: Per_R44_C47

description: P3_Per.txt (matrix)


title: Per_R44_C41

description: P3_Per.txt (matrix)


title: Per_R44_C20

description: P3_Per.txt (matrix)


title: Per_R44_C23

description: P3_Per.txt (matrix)


title: Per_R44_C17

description: P3_Per.txt (matrix)


title: Per_R44_C15

description: P3_Per.txt (matrix)


title: Per_R44_C19

description: P3_Per.txt (matrix)


title: Per_R43_C71

description: P3_Per.txt (matrix)


title: Per_R43_C70

description: P3_Per.txt (matrix)


title: Per_R43_C69

description: P3_Per.txt (matrix)


title: Per_R43_C61

description: P3_Per.txt (matrix)


title: Per_R43_C64

description: P3_Per.txt (matrix)


title: Per_R43_C62

description: P3_Per.txt (matrix)


title: Per_R43_C45

description: P3_Per.txt (matrix)


title: Per_R43_C39

description: P3_Per.txt (matrix)


title: Per_R43_C43

description: P3_Per.txt (matrix)


title: Per_R43_C20

description: P3_Per.txt (matrix)


title: Per_R43_C23

description: P3_Per.txt (matrix)


title: Per_R43_C38

description: P3_Per.txt (matrix)


title: Per_R43_C18

description: P3_Per.txt (matrix)


title: Per_R42_C65

description: P3_Per.txt (matrix)


title: Per_R42_C42

description: P3_Per.txt (matrix)


title: Per_R42_C23

description: P3_Per.txt (matrix)


title: Per_R42_C61

description: P3_Per.txt (matrix)


title: Per_R42_C41

description: P3_Per.txt (matrix)


title: Per_R42_C21

description: P3_Per.txt (matrix)


title: Per_R42_C20

description: P3_Per.txt (matrix)


title: Per_R42_C16

description: P3_Per.txt (matrix)


title: Per_R42_C13

description: P3_Per.txt (matrix)


title: Per_R42_C17

description: P3_Per.txt (matrix)


title: Per_R41_C66

description: P3_Per.txt (matrix)


title: Per_R41_C68

description: P3_Per.txt (matrix)


title: Per_R41_C70

description: P3_Per.txt (matrix)


title: Per_R42_C14

description: P3_Per.txt (matrix)


title: Per_R41_C62

description: P3_Per.txt (matrix)


title: Per_R41_C47

description: P3_Per.txt (matrix)


title: Per_R41_C63

description: P3_Per.txt (matrix)


title: Per_R41_C65

description: P3_Per.txt (matrix)


title: Per_R42_C68

description: P3_Per.txt (matrix)


title: Per_R41_C44

description: P3_Per.txt (matrix)


title: Per_R41_C36

description: P3_Per.txt (matrix)


title: Per_R41_C20

description: P3_Per.txt (matrix)


title: Per_R40_C47

description: P3_Per.txt (matrix)


title: Per_R40_C70

description: P3_Per.txt (matrix)


title: Per_R41_C19

description: P3_Per.txt (matrix)


title: Per_R40_C71

description: P3_Per.txt (matrix)


title: Per_R40_C43

description: P3_Per.txt (matrix)


title: Per_R40_C42

description: P3_Per.txt (matrix)


title: Per_R3_C47

description: P3_Per.txt (matrix)


title: Per_R3_C44

description: P3_Per.txt (matrix)


title: Per_R3_C62

description: P3_Per.txt (matrix)


title: Per_R3_C40

description: P3_Per.txt (matrix)


title: Per_R3_C39

description: P3_Per.txt (matrix)


title: Per_R3_C16

description: P3_Per.txt (matrix)


title: Per_R3_C18

description: P3_Per.txt (matrix)


title: Per_R39_C67

description: P3_Per.txt (matrix)


title: Per_R39_C64

description: P3_Per.txt (matrix)


title: Per_R39_C19

description: P3_Per.txt (matrix)


title: Per_R39_C13

description: P3_Per.txt (matrix)


title: Per_R39_C16

description: P3_Per.txt (matrix)


title: Per_R39_C62

description: P3_Per.txt (matrix)


title: Per_R39_C37

description: P3_Per.txt (matrix)


title: Per_R40_C60

description: P3_Per.txt (matrix)


title: Per_R40_C61

description: P3_Per.txt (matrix)


title: Per_R38_C66

description: P3_Per.txt (matrix)


title: Per_R39_C12

description: P3_Per.txt (matrix)


title: Per_R40_C22

description: P3_Per.txt (matrix)


title: Per_R38_C64

description: P3_Per.txt (matrix)


title: Per_R38_C21

description: P3_Per.txt (matrix)