title: KD3

city: Charleston

first: Deepak

last: Nihalani

state: SC

address: 70 President street

department: Medicine

institute: Medical University of South Carolina

data_processing:
Downstream bioinformatics analyses was performed by using a combination of programs including Bowtie2, Tophat2, HTseq and Cufflink .
Reference genome and gene model annotation files were acquired from NCBI/UCSC/Ensemble genome browser.
Indexes of the reference genome were built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
Gene expression level quantification was done using HTSeq v0.6.1 and for each gene read numbers counts were mapped, whereas, Reads Per Kilobase of exon model (RPKM) of each gene was calculated based on the length of the gene and expression levels were analyzed
DESeq2 R package (2_1.6.3) database was used for the differential expression (DE) analyses. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach and adjusted P-value <0.05 found by DESeq2 were assigned as DE. Analyses of DE of two conditions was performed using the DEGSeq R package (1.12.0). The P-values were also adjusted using Benjamini & Hochberg method. Corrected P-value of 0.005 and log2 (Fold change) of 1 were set as threshold for significantly differential expression.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Kidney cell line

extract_protocol:
RNA samples were isolated from independent experiments performed in triplicate using Qiagen RNAeasy Mini Kit.
RNA libraries were prepared for sequencing using standard HiSeq/MiSeq Illumina platform for the RNA sequencing

tag: genotype/variation

value: Eoxc5 knockdown


title: siRNA RNA-seq from MCF-7 (ENCLB934RMS)

status: Public on Mar 02 2019

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR005AHI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on MCF-7 cells treated with siRNA targeting ZFX.
experiment encode accession: ENCSR005AHI
assay title: siRNA RNA-seq
assembly: hg19, GRCh38
possible controls: ENCSR783OQM
encode release date: 2017-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB934RMS
size range: >200

library_source: transcriptomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens MCF-7 cell line expressing RNAi targeting ZFX

tag: antibody

value: ZFX

tag: line

value: cell line

tag: description

value: MCF-7 cells treated with a siRNA knockdown against ZFX, used in RNA-seq experiments.

tag: biosample encode accession

tag: Sex

value: female

tag: health state

value: breast cancer (adenocarcinoma)

tag: dev stage

value: adult

tag: age

value: 69 year

tag: lab

value: Peggy Farnham, USC

tag: link

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCBS230HRE at ENCODE; https://www.encodeproject.org/ENCBS230HRE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; https://web.expasy.org/cellosaurus/CVCL_0031


title: WGBS from testis (ENCLB904LWN)

description:
https://www.encodeproject.org/experiments/ENCSR011HZJ/
***************
biological replicate number: 1
technical replicate number: 1
description: WGBS on testis
experiment encode accession: ENCSR011HZJ
assay title: WGBS
assembly: GRCh38
encode release date: 2018-01-18
lab: Richard Myers, HAIB
library encode accession: ENCLB904LWN

library_source: genomic

molecule: genomic DNA

source_name: Homo sapiens male adult (54 years) testis tissue

value: testis

value: tissue

value: male

value: 54 year

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/

value: ENCBS955OSA at ENCODE; https://www.encodeproject.org/ENCBS955OSA/


title: ChIP-seq from liver (ENCLB377FLO)

description:
https://www.encodeproject.org/experiments/ENCSR635OSG/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD21 ChIP-seq on human liver
experiment encode accession: ENCSR635OSG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR221IDN
encode release date: 2017-04-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB377FLO
size range: 150-350

source_name: Homo sapiens liver tissue female child (6 years)

value: liver

value: Human liver Tissue obtained from a healthy 6 year old Caucasian female donor

value: 6 year

value: child

value: healthy

value: Thomas Gingeras, CSHL

value: ENCBS045RNA at ENCODE; https://www.encodeproject.org/ENCBS045RNA/

value: Derived from ENCODE donor ENCDO059AAA; https://www.encodeproject.org/ENCDO059AAA/

value: ENCODE dbxrefs Liver_STL004; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=Liver_STL004


title: CRISPRi RNA-seq from K562 (ENCLB851VUS)

description:
https://www.encodeproject.org/experiments/ENCSR016WFQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated by CRISPR interference for a non-specific target (batch C control).
experiment encode accession: ENCSR016WFQ
assay title: CRISPRi RNA-seq
assembly: hg19, GRCh38
encode release date: 2017-11-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB851VUS
size range: >200

source_name: Homo sapiens K562 cell line genetically modified (interference) using CRISPR targeting Non-specific target control

value: Control

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Sherman Weissman, Yale

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCBS287NAE at ENCODE; https://www.encodeproject.org/ENCBS287NAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; https://web.expasy.org/cellosaurus/CVCL_0004


title: human_MAb_PvDBPII_specific_recomb_IgG1 (087085)

type: protein

city: Cleveland

first: Christopher

middle: L

last: King

state: Ohio

address: 2109 Adelbert Road 4th Floor

department: Center for Global Health & Diseases

institute: Case Western Reserve University

hyb_protocol: Monoclonal antibodies prepared at 10 ng/ml in protein array blocking buffer (Maine Manufacturing, Sanford, ME). Serum sample was diluted 1:100 in protein array blocking buffer supplemented with E. coli lysate (GenScript, Piscataway, NJ) to a final concentration of 10mg/ml, and pre-incubated at room temperature (RT) for 30 min. Concurrently, arrays were rehydrated in blocking buffer (without lysate) for 30 min. Blocking buffer was removed, and arrays were probed with samples using sealed chambers to ensure no cross-contamination of sample between pads. Arrays were incubated over-night at 4 °C with gentle agitation. Arrays were then washed at RT five times with TBS-0.05% Tween 20 (T-TBS), followed by incubation with biotin-conjugated goat anti-human IgG (Jackson ImmunoResearch, West Grove, PA) diluted 1:200 in blocking buffer for 1 h at RT. After incubation in secondary antibodies, arrays were then washed three times with T-TBS, followed by incubation with QDot® 800 Streptavidin Conjugate (Molecular Probes by Life Technologies, Eugene, Oregon, USA,) for 45 min at RT protected from light. Arrays were washed three times with T-TBS, and once with water. Chips were air dried by centrifugation at 1,000 g for 5 min and scanned on ArrayCam™ 400-S Microarray Imaging System from Grace Bio-Labs (Bend, OR). Spot and background intensities were measured using an annotated grid (.gal) file. ArrayCam™settings were set at 50 gain, and the exposure time 50ms.

scan_protocol: ArrayCam 400-S Microarray Imaging System from Grace Bio-Labs (Bend, OR), settings were set at 50 gain, and the exposure time 50 (ms). Spot and background intensities were measured using an annotated grid (.gal) file. single wavelength excitation at 800nm, automated software  provides spot finding and data.

data_processing: the mean background signal of antibody binding to 24 control spots of in vitro transcription/translation reaction without DNA template (noDNA spots) were removed from each samples raw values of antibody binding measured as the mean pixel intensity of spots of printed protein

molecule: protein

source_name: recombinant antibody,IgG1

label_protocol: The primary antibody used for arrays was biotin-conjugated goat anti-human IgG from Jackson Immunoresearch (872 W Baltimore Pike, West Grove, PA 19390 USA). Detection by QDot 800 Streptavidin Conjugate.

growth_protocol: H+L plasmids PEI transient transfection using Expi293 (Life Technologies) cells in suspension

extract_protocol: Protein A column purification of epi293 cell supernatant

tag: human antibody

value: monoclonal

tag: h+l transfection

value: produced by transient transfection using Expi293 (Life Technologies) cells in suspension

tag: country origin h+l

value: Cambodia


title: ChIP-seq from H1-hESC (ENCLB527MZB)

description:
https://www.encodeproject.org/experiments/ENCSR633XNG/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on human H1-hESC
experiment encode accession: ENCSR633XNG
assay title: ChIP-seq
assembly: GRCh38, hg19
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB527MZB
size range: 150-350

source_name: Homo sapiens H1-hESC cell line

value: male

value: healthy

value: embryonic

value: unknown

value: Michael Snyder, Stanford

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/

value: ENCBS270AGK at ENCODE; https://www.encodeproject.org/ENCBS270AGK/

value: ENCODE dbxrefs Cellosaurus CVCL_9771; https://web.expasy.org/cellosaurus/CVCL_9771


title: KD2

value: Eoxc5 knockdown


title: Heterokaryon 48h

city: Blacksburg

first: M. Cristina

last: Villafranca

state: VA

address: 205 Duckpond Drive

institute: Virginia Polytechnic Institute and State University

description:
Final_BovineReads_bFF_24_48_72.xlsx
Final_MouseReads_mESC_24_48_72.xlsx

data_processing:
MiSeq Fastq files uploaded to Geneious version 8.
Geneious used to align all reads to the bovine and mouse NCBI Reference Sequence (NCBI RefSeq NM_ and NR_ genes only (35,814 mouse genes and 14,234 Cow genes); retrieved on June 2017), using the “Map to Reference” option (with a custom setting allowing for 2% error, and the “Map Multiple Matches” option set to “random”.
Number of reads aligning to each gene (by species) exported to Microsoft Excel, resulting in one spreadsheet for mouse reads, and one for bovine reads.
Read counts were normalized to reads per million mapped reads (RPM).
Genome_build: Bovine assembly UMD_3.1.1/bosTau8
Genome_build: Mouse assembly GRCm38/mm10
Supplementary_files_format_and_content: Two .xlsx files containing read counts by species (mouse and bovine). Each file contains gene name, gene ID, read counts, and normalized expression (RPM).

molecule: polyA RNA

organism:
Bos taurus
Mus musculus

source_name: bovine fetal fibroblast,mouse embryonic stem cell C57BL

growth_protocol: Bovine fetal fibroblasts (bFFs) were isolated from an abattoir-obtained male fetus of unknown genetic background at approximately gestation day 60, and cultured in fibroblast medium consisting of Dulbecco's Modified Eagle's Medium (DMEM; Gibco) with 10% fetal bovine serum (FBS; HyClone) and 50 ug/ml Gentamycin (Lonza) in a 5% CO2 in air incubator at 38.5°C. Mouse embryonic stem (mES) cells from the line C57BL/6 were purchased from ATCC (CRL-1002) and cultured on a monolayer of gamma irradiated mouse embryonic fibroblasts (IRR-MEFs, StemGent) in mES cell medium: DMEM with 15% ESC-qualified FBS (Gibco), 1X Non-Essential Amino Acids (HyClone), 1X Glutamax (Gibco), 1,500 U/ml of ESGRO (Millipore), 0.55 mM beta-mercaptoethanol (Sigma), 1 µM PD0325901 (PD; Cayman chemical company), 3 µM CHIR99021 (CHIR; Cayman chemical company), and 50 µg/ml Gentamycin (Lonza) in a 5% CO2 in air incubator at 37°C. After fusion, co-cultured bFFs and mES cells were incubated in basic ES cell medium: DMEM with 15% ESC-qualified FBS (Gibco), 1X Non-Essential Amino Acids (HyClone), 1X Glutamax (Gibco), 1,500 U/ml of ESGRO (Millipore), 0.55 mM beta-mercaptoethanol (Sigma), and 50 µg/ml Gentamycin (Lonza) in a 5% CO2 in air incubator at 37°C until analysis.

extract_protocol:
For each sample, 200 cells of the respective type were isolated using ImageStream and FACS. cDNA was generated from intact cells, using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, following the manufacturer’s instructions for cDNA production using cells as starting material. We used 14 cycles for cDNA amplification.
Libraries were prepared using the Accel-NGS® 2S Plus DNA Library Kit (Swift biosciences).

treatment_protocol: A total of 2x10e5 bFFs were seeded in one well of a 24-well plate in basic ES cell medium, and 2 h later 6x10e5 mES cells were seeded in the same well. Cells were co-cultured for 4h before fusion. Fusion was performed by adding a mixture of 280 µl PEG with 20 µl DMSO, pre-warmed to 37°C to each well during exactly 2 min at room temperature, followed by 2 washes with DPBS and 1 wash with basic ES cell medium. Cells were cultured at 37°C in basic ES cell medium until isolation and analysis.

tag: strain

tag: treatment

value: fused

tag: sampling time after fusion

tag: cell type

value: bi-species (mouse/bovine) heterokaryon


title: human_MAb_PvDBPII_specific_recomb_IgG1 (081082)


title: KD1

tag: genotype/variation


title: Ctrl4

value: wild type


title: RLT rep3

city: Hangzhou

first: Jiang

last: Penglei

address: Yuhangtang Road 866

department: School of basic medicine science

country: China

institute: Zhejiang University

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw reads were trimmed and filtered using Seqtk (https://github.com/lh3/seqtk). Low quality (Q < 20) bases were trimmed from 3’ ends of the reads and the trimmed reads were filtered with read length ≥ 25 bp.
Clean RNA-Seq reads for each sample were aligned by HISAT2 (2.0.4) with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 (Danio_rerio.GRCz10.84.gtf) (1).
The number of reads mapped to the genes was counted by StringTie and normalized by TMM (trimmed mean of M values) method(2). We next calculated fragments per kilobase per million mapped reads (FPKM) of each gene to indicate gene expression level.
Genome_build: GRCz10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene

organism: Danio rerio

source_name: muscle tissues

growth_protocol: Breeding fish were maintained at 28°C in a circulating water system on a 14-h light/10-h dark cycle. Embryos were collected by natural spawning and staged.

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (15596-018, Life technologies) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNAClean XP Kit (A63987, Beckman Coulter)and RNase-Free DNase Set (79254, QIAGEN).
Libraries were constructed using VAHTS Total RNA-Seq（H/M/R) Library PrepKit for Illumina (NR603-02, Vazyme).
Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150-bp paired-end sequencing reads.

treatment_protocol: Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf, followed by the removal of the drug using three rinses, the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO.

tag: tissue

value: muscle

value: radicicol


title: ChIP-seq from HepG2 (ENCLB555ADC)

description:
https://www.encodeproject.org/experiments/ENCSR101FJS/
***************
biological replicate number: 1
technical replicate number: 1
description: TBL1XR1 ChIP-seq on human HepG2
experiment encode accession: ENCSR101FJS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR613TDP
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB555ADC
size range: 150-350

source_name: Homo sapiens HepG2 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7e85e27a-1b03-493d-b73f-db4ce2246318/@@download/attachment/wgEncodeSydhHistone.release3.html.pdf, general protocol: https://www.encodeproject.org/documents/0612f0bf-3665-47f8-af5d-09aab3d4ca24/@@download/attachment/wgEncodeSydhTfbs.release3.html.pdf

tag: antibody

tag: line

value: cell line

tag: description

value: Hepatocellular carcinoma

value: child

value: 15 year

value: hepatocellular carcinoma

value: ENCBS522AAA at ENCODE; https://www.encodeproject.org/ENCBS522AAA/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: human_MAb_PvDBPII_specific_recomb_IgG1 (071063)

value: monoclonal

value: produced by transient transfection using Expi293 (Life Technologies) cells in suspension

value: Cambodia


title: ChIP-seq from HepG2 (ENCLB555ADD)

description:
https://www.encodeproject.org/experiments/ENCSR101FJS/
***************
biological replicate number: 2
technical replicate number: 1
description: TBL1XR1 ChIP-seq on human HepG2
experiment encode accession: ENCSR101FJS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR613TDP
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB555ADD
size range: 150-350

tag: biosample encode accession

tag: Sex

value: male

value: Michael Snyder, Stanford

tag: health state

value: ENCBS523AAA at ENCODE; https://www.encodeproject.org/ENCBS523AAA/


title: ChIP-seq from A549 (ENCLB267TJL)

description:
https://www.encodeproject.org/experiments/ENCSR067HGI/
***************
biological replicate number: 1
technical replicate number: 1
description: CHD2 ChIP-seq on human A549
experiment encode accession: ENCSR067HGI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR949BZP, ENCSR496AXR
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB267TJL
size range: 150-350

source_name: Homo sapiens A549 immortalized cell line

value: epithelial cell line derived from a 58 year old caucasian male lung carcinoma.

tag: dev stage

value: adult

tag: age

value: 58 year

tag: lab

value: ENCBS159AAA at ENCODE; https://www.encodeproject.org/ENCBS159AAA/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023

value: ENCODE dbxrefs A549; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=A549

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-185.aspx


title: ChIP-seq from liver (ENCLB378GGD)

description:
https://www.encodeproject.org/experiments/ENCSR635OSG/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIP-seq on human liver
experiment encode accession: ENCSR635OSG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR221IDN
encode release date: 2017-04-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB378GGD
size range: 150-350

source_name: Homo sapiens liver tissue male adult (32 years)

value: liver

value: tissue

value: Human liver Tissue obtained from a healthy, 32 year old Caucasian male donor

value: 32 year

value: healthy with non-obstructive CAD (coronary artery disease)

value: Thomas Gingeras, CSHL

tag: link

value: ENCBS046RNA at ENCODE; https://www.encodeproject.org/ENCBS046RNA/

value: Derived from ENCODE donor ENCDO060AAA; https://www.encodeproject.org/ENCDO060AAA/

value: ENCODE dbxrefs Liver_STL011; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=Liver_STL011


title: human_MAb_PvDBPII_specific_recomb_IgG1 (055056)

tag: human antibody

value: monoclonal

tag: h+l transfection

value: produced by transient transfection using Expi293 (Life Technologies) cells in suspension

tag: country origin h+l

value: Cambodia


title: RLT rep2

value: muscle

tag: treatment

value: radicicol


title: RLT rep1


title: Ctrl2

value: wild type


title: ChIP-seq from A549 (ENCLB767KVU)

description:
https://www.encodeproject.org/experiments/ENCSR067HGI/
***************
biological replicate number: 3
technical replicate number: 1
description: CHD2 ChIP-seq on human A549
experiment encode accession: ENCSR067HGI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR949BZP, ENCSR496AXR
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB767KVU
size range: 150-350

value: cell line

value: epithelial cell line derived from a 58 year old caucasian male lung carcinoma.

value: adult

value: male

value: 58 year

value: Michael Snyder, Stanford

value: ENCBS127GWZ at ENCODE; https://www.encodeproject.org/ENCBS127GWZ/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: WT rep3

value: DMSO


title: human_MAb_PvDBPII_specific_recomb_IgG1 (065098)


title: Heterokaryon 24h

tag: strain

value: fused

tag: sampling time after fusion

tag: cell type

value: bi-species (mouse/bovine) heterokaryon


title: human_MAb_PvDBPII_specific_recomb_IgG1 (088084)

value: monoclonal

value: produced by transient transfection using Expi293 (Life Technologies) cells in suspension


title: WT rep1

tag: tissue

value: muscle


title: WT rep2


title: ChIP-seq from K562 (ENCLB711TFY)

description:
https://www.encodeproject.org/experiments/ENCSR038DJJ/
***************
biological replicate number: 1
technical replicate number: 1
description: SMAD1 ChIP-seq on human K562
experiment encode accession: ENCSR038DJJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR080EOT
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB711TFY
size range: 150-350

source_name: Homo sapiens K562 immortalized cell line

tag: antibody

tag: line

value: Leukemia, the continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS489ZOH at ENCODE; https://www.encodeproject.org/ENCBS489ZOH/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: bFF only

organism: Bos taurus

source_name: bovine fetal fibroblast

value: control

value: bovine fetal fibroblast


title: ChIP-seq from K562 (ENCLB114XYD)

description:
https://www.encodeproject.org/experiments/ENCSR038DJJ/
***************
biological replicate number: 2
technical replicate number: 1
description: SMAD1 ChIP-seq on human K562
experiment encode accession: ENCSR038DJJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR080EOT
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB114XYD
size range: 150-350

value: cell line

tag: description

tag: biosample encode accession

value: adult

value: Michael Snyder, Stanford

value: ENCBS118YJZ at ENCODE; https://www.encodeproject.org/ENCBS118YJZ/


title: human_MAb_PvDBPII_specific_recomb_IgG1 (053054)

value: monoclonal

value: Cambodia


title: human_MAb_TTCF_specific_recomb_IgG1

value: produced by transient transfection using Expi293 (Life Technologies) cells in suspension

value: United States


title: ASD19_0_5

city: Leiden

first: Mariana

last: Avalos Garcia

address: Sylviusweg 72

department: Microbial Biotechnology and Health

country: Netherlands

institute: Leiden University/Biology Institute Leiden

data_processing:
single end sequence generated using Illumina HiSeq2500 system. FastQ sequence files using Illumina Casava pipeline version 1.8.3. Initial quality assesment passing the Illumina chastity filtering. Second quality assesment using the FASTQC quality control tool version 0.10.0
FASTQ sequences quality was enhanced by trimming off low quality bases using CLC Genomics workbench version 8.0
Expresion measure was RPKM and statistical analysis was performed using Kal's Z-test
Genome_build: NC_012967
Supplementary_files_format_and_content: expression tables in excel format (*rnaseq-table.xlsx) and normalized expression values between samples (*rnaseq-comparison_final.xlsx)

organism: Escherichia coli

source_name: Escherichia coli cells

growth_protocol: E. coli cells were routinely grown on LB liquid media until an O.D.600 of 0.5

extract_protocol:
Cells were mixed with RNA protect bacterial reagent, RNA was extracted by a standard method of hot phenol/chloroform/isoamyl alcohol
RNA libraries were prepared for sequencing using standard Illumina protocols


title: shEWS_6hrs_rep2

status: Public on Mar 01 2019

type: RNA

city: La Jolla

first: Richard

last: Virgen-Slane

address: 10901 North Torrey Pines Rd

department: Infectious and Inflammatory Diseases Center

institute: Sanford Burnham Prebys Medical Discovery Institute

description: nCounter Human Inflammation panel V2

hyb_protocol: Hybridization carried out according to manufacturer's protocol

scan_protocol: Scanning carried out according to manufacturer's protocol

data_processing: Raw counts were accessed using nSolver Analysis Software 3.0 and imported into R for differential expression using the DeSeq2 package. Time (h) dependent changes following LTβR stimulation were modeled as sequential differences ([2-0 (h) and 6-2 (h)] using the MASS package in R.

label: biotin

source_name: EWS targeting shRNA, LTBR stimulation 6 hrs

label_protocol: Labeling carried out according to manufacturer's protocol

growth_protocol: 100,000 fibroblasts were plated expressing either control or EWS-targeting shRNAs (6 well format) in DMEM with 10% FBS at 37ºC.

extract_protocol: Following stimulation for the indicated times, monolayers were washed with cold PBS, and lysed with QIAGEN RLT buffer. RNA was isolated using QIAGEN RNA easy extraction protocol

treatment_protocol: Two days following plating, cells were stimulated with 2 µg/ml agonistic goat anti-human LTBR antibody for 0, 2, or 6 hours

tag: genotype

value: EWS knockdown

value: LTBR stimulation

tag: time

value: 6 hr


title: shEWS_2hrs_rep2

description: nCounter Human Inflammation panel V2

source_name: EWS targeting shRNA, LTBR stimulation 2 hrs

value: 2 hr


title: shEWS_2hrs_rep1

description: nCounter Human Inflammation panel V2


title: shEWS_0hrs_rep2

description: nCounter Human Inflammation panel V2

source_name: EWS targeting shRNA, LTBR stimulation 0 hrs


title: shCON_6hrs_rep2

description: nCounter Human Inflammation panel V2

source_name: Control shRNA, LTBR stimulation 6 hrs


title: shEWS_0hrs_rep1

description: nCounter Human Inflammation panel V2


title: 9a_0_5


title: shCON_2hrs_rep1

description: nCounter Human Inflammation panel V2

source_name: Control shRNA, LTBR stimulation 2 hrs


title: shCON_2hrs_rep2

description: nCounter Human Inflammation panel V2


title: shCON_0hrs_rep2

description: nCounter Human Inflammation panel V2

source_name: Control shRNA, LTBR stimulation 0 hrs


title: shCON_0hrs_rep1

description: nCounter Human Inflammation panel V2


title: SA1001 Sarcoma

city: Kamakura

first: Ichikawa

last: Makiko

state: Kanagawa

country: Japan

institute: Toray Industries, Inc.

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetEsophageal Cancerted) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

source_name: serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: disease state

value: Sarcoma

tag: Sex

value: Male

tag: age

tag: ctstage

value: uncertain

tag: cnstage

tag: cmstage


title: shEWS_6hrs_rep1

description: nCounter Human Inflammation panel V2

tag: treatment


title: Rh-30 siB7-H3

city: Kyoto

first: Takuyo

last: Kanayama

address: 465, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

department: Department of Pediatrics

institute: Kyoto Prefectural University of Medicine

description: Rh-30 transfected by siB7-H3

hyb_protocol: Biotin-labeled cRNA was hybridized to GeneChip Human Genome U133 Plus 2.0 Array.

scan_protocol: Hybridized arrays were stained and scanned with a Genechip 3000 7G Scanner.

data_processing: Data were analyzed with Affymetrix Expression Console Software 1.4.1.

source_name: Rh-30, rhabdomyosarcoma cell line

label_protocol: Biotin labeled

growth_protocol: Rh-30 were maintained in RPMI 1640 medium, supplemented with 10% fetal bovine serum , penicillin (100 U/mL) and streptomycin (100 μg/mL) at 37℃ in a humidified atmosphere of 5% CO2.

extract_protocol: Total RNA was extracted from rhabdomyosarcoma cell lines using RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: siRNA transfections were carried out using Lipofectamine RNAiMAX (Invitrogen) according to manufacturer’s recommended procedures. The final concentration of siRNAs was 5 nM.

value: Rhabdomyosarcoma cell line


title: Rh-30 siControl

description: Rh-30 transfected by siControl


title: SA0967 Sarcoma


title: SA0981 Sarcoma


title: SA0868 Sarcoma


title: SA0887 Sarcoma


title: SA0922 Sarcoma


title: Rh-30 siPAX3-FOXO1

description: Rh-30 transfected by siPAX3-FOXO1


title: SA0878 Sarcoma


title: SA0944 Sarcoma


title: shCON_6hrs_rep1

description: nCounter Human Inflammation panel V2

value: control


title: SA0835 Sarcoma


title: SA0468 Sarcoma


title: SA0863 Sarcoma


title: SA0394 Sarcoma


title: SA0384 Sarcoma


title: SA0378 Sarcoma


title: SA0369 Sarcoma


title: SA0364 Sarcoma


title: SA0368 Sarcoma


title: SA0923 Sarcoma


title: SA0353 Sarcoma


title: SA0342 Sarcoma


title: SA0341 Sarcoma


title: human_MAb_PvDBPII_specific_recomb_IgG1 (080064)

source_name: recombinant antibody,IgG1

tag: human antibody

tag: h+l transfection

tag: country origin h+l


title: SA0331 Sarcoma


title: SA0326 Sarcoma


title: SA0329 Sarcoma


title: SA0310 Sarcoma


title: SA0305 Sarcoma


title: SA0298 Sarcoma


title: SA0301 Sarcoma


title: SA0294 Sarcoma


title: SA0302 Sarcoma


title: SA0280 Sarcoma


title: SA0287 Sarcoma


title: SA0282 Sarcoma


title: SA0267 Sarcoma


title: SA0215 Sarcoma


title: SA0279 Sarcoma


title: SA0268 Sarcoma


title: SA0123 Sarcoma


title: SA0183 Sarcoma


title: SA0187 Sarcoma


title: SA0105 Sarcoma


title: SA0202 Sarcoma


title: SA0108 Sarcoma


title: SA0094 Sarcoma


title: SA0063 Sarcoma


title: SA0055 Sarcoma


title: PR1043 Prostate Cancer

value: Prostate Cancer


title: PR1038 Prostate Cancer


title: PR1042 Prostate Cancer


title: PR1039 Prostate Cancer


title: Ctrl1

source_name: Kidney cell line

tag: genotype/variation

value: wild type


title: PR1040 Prostate Cancer


title: PR1035 Prostate Cancer


title: PR1034 Prostate Cancer


title: SA0167 Sarcoma


title: PR1044 Prostate Cancer


title: PR1033 Prostate Cancer


title: PR1030 Prostate Cancer


title: PR1025 Prostate Cancer


title: SA0181 Sarcoma


title: PR1027 Prostate Cancer


title: PR1029 Prostate Cancer


title: PR1021 Prostate Cancer


title: PR1019 Prostate Cancer


title: PR1014 Prostate Cancer


title: PR1011 Prostate Cancer


title: PR1016 Prostate Cancer


title: PR1041 Prostate Cancer


title: PR1012 Prostate Cancer


title: PR1037 Prostate Cancer


title: PR1008 Prostate Cancer


title: PR1013 Prostate Cancer


title: PR1010 Prostate Cancer


title: PR1015 Prostate Cancer


title: PR1003 Prostate Cancer


title: PR1028 Prostate Cancer


title: PR1031 Prostate Cancer


title: PR1006 Prostate Cancer


title: PR1007 Prostate Cancer


title: PR1036 Prostate Cancer


title: PR1002 Prostate Cancer


title: PR1004 Prostate Cancer


title: PR1009 Prostate Cancer


title: PR0995 Prostate Cancer


title: PR0994 Prostate Cancer


title: PR1001 Prostate Cancer


title: PR0996 Prostate Cancer


title: PR0990 Prostate Cancer


title: PR0984 Prostate Cancer


title: PR0987 Prostate Cancer


title: PR0985 Prostate Cancer


title: PR0981 Prostate Cancer


title: PR0982 Prostate Cancer


title: PR0980 Prostate Cancer


title: PR0976 Prostate Cancer


title: PR0993 Prostate Cancer


title: PR0986 Prostate Cancer


title: PR0979 Prostate Cancer


title: PR0983 Prostate Cancer


title: PR0975 Prostate Cancer


title: PR0989 Prostate Cancer


title: PR0978 Prostate Cancer


title: PR0972 Prostate Cancer


title: PR0971 Prostate Cancer


title: PR0973 Prostate Cancer


title: SA0976 Sarcoma


title: PR0977 Prostate Cancer


title: PR0969 Prostate Cancer


title: PR0961 Prostate Cancer


title: PR0959 Prostate Cancer


title: PR0967 Prostate Cancer


title: PR0958 Prostate Cancer


title: PR0954 Prostate Cancer


title: PR0952 Prostate Cancer


title: PR0968 Prostate Cancer


title: PR0966 Prostate Cancer


title: PR0956 Prostate Cancer


title: PR0950 Prostate Cancer


title: PR0964 Prostate Cancer


title: PR0962 Prostate Cancer


title: PR0947 Prostate Cancer


title: PR0970 Prostate Cancer


title: PR0960 Prostate Cancer


title: PR1032 Prostate Cancer


title: PR0999 Prostate Cancer


title: PR0951 Prostate Cancer


title: PR0948 Prostate Cancer


title: PR0940 Prostate Cancer


title: PR0942 Prostate Cancer


title: PR0938 Prostate Cancer


title: PR0945 Prostate Cancer


title: PR0944 Prostate Cancer


title: SA0324 Sarcoma


title: PR0939 Prostate Cancer


title: PR0941 Prostate Cancer


title: PR0934 Prostate Cancer


title: PR0943 Prostate Cancer


title: PR0936 Prostate Cancer


title: PR0926 Prostate Cancer


title: PR0925 Prostate Cancer


title: PR0955 Prostate Cancer


title: PR0929 Prostate Cancer


title: PR0932 Prostate Cancer


title: PR0931 Prostate Cancer


title: PR0917 Prostate Cancer


title: PR0918 Prostate Cancer


title: PR0915 Prostate Cancer


title: PR0930 Prostate Cancer


title: PR0924 Prostate Cancer


title: PR0920 Prostate Cancer


title: PR0921 Prostate Cancer


title: PR0916 Prostate Cancer


title: PR0923 Prostate Cancer


title: PR0919 Prostate Cancer


title: PR0927 Prostate Cancer


title: PR0935 Prostate Cancer


title: PR0912 Prostate Cancer


title: PR0909 Prostate Cancer


title: PR0910 Prostate Cancer


title: PR0902 Prostate Cancer


title: PR0897 Prostate Cancer


title: PR0898 Prostate Cancer


title: PR0896 Prostate Cancer


title: PR0890 Prostate Cancer


title: PR0892 Prostate Cancer


title: PR0894 Prostate Cancer


title: PR0906 Prostate Cancer


title: PR0908 Prostate Cancer


title: PR0911 Prostate Cancer


title: PR0904 Prostate Cancer


title: PR0903 Prostate Cancer


title: PR0907 Prostate Cancer


title: PR0913 Prostate Cancer


title: PR0887 Prostate Cancer


title: PR0885 Prostate Cancer


title: PR0889 Prostate Cancer


title: PR0900 Prostate Cancer


title: PR0886 Prostate Cancer


title: PR0881 Prostate Cancer


title: PR0872 Prostate Cancer


title: PR0871 Prostate Cancer


title: PR0860 Prostate Cancer


title: PR0864 Prostate Cancer


title: PR0863 Prostate Cancer


title: PR0862 Prostate Cancer


title: PR0870 Prostate Cancer


title: PR0882 Prostate Cancer


title: PR0856 Prostate Cancer


title: PR0859 Prostate Cancer


title: PR0847 Prostate Cancer


title: PR0857 Prostate Cancer


title: PR0845 Prostate Cancer


title: PR0879 Prostate Cancer


title: PR0853 Prostate Cancer


title: PR0833 Prostate Cancer


title: PR0834 Prostate Cancer


title: PR0850 Prostate Cancer


title: PR0851 Prostate Cancer


title: PR0846 Prostate Cancer


title: PR0849 Prostate Cancer


title: PR0840 Prostate Cancer


title: PR0866 Prostate Cancer


title: PR0828 Prostate Cancer


title: PR0821 Prostate Cancer


title: PR0823 Prostate Cancer


title: PR0820 Prostate Cancer


title: PR0819 Prostate Cancer


title: PR0818 Prostate Cancer


title: PR0817 Prostate Cancer


title: PR0813 Prostate Cancer


title: PR0815 Prostate Cancer


title: PR0810 Prostate Cancer


title: PR0812 Prostate Cancer


title: PR0806 Prostate Cancer


title: PR0825 Prostate Cancer


title: PR0807 Prostate Cancer


title: PR0808 Prostate Cancer


title: PR0829 Prostate Cancer


title: PR0794 Prostate Cancer


title: PR0795 Prostate Cancer


title: PR0797 Prostate Cancer


title: PR0800 Prostate Cancer


title: PR0789 Prostate Cancer


title: PR0792 Prostate Cancer


title: PR0811 Prostate Cancer


title: PR0838 Prostate Cancer


title: PR0791 Prostate Cancer


title: PR0793 Prostate Cancer


title: PR0802 Prostate Cancer


title: PR0782 Prostate Cancer


title: PR0781 Prostate Cancer


title: PR0780 Prostate Cancer


title: PR0809 Prostate Cancer


title: PR0790 Prostate Cancer


title: PR0769 Prostate Cancer


title: PR0768 Prostate Cancer


title: PR0776 Prostate Cancer


title: PR0778 Prostate Cancer


title: PR0773 Prostate Cancer


title: PR0770 Prostate Cancer


title: PR0758 Prostate Cancer


title: PR0764 Prostate Cancer


title: PR0759 Prostate Cancer


title: PR0767 Prostate Cancer


title: PR0752 Prostate Cancer


title: PR0751 Prostate Cancer


title: PR0766 Prostate Cancer


title: PR0756 Prostate Cancer


title: PR0748 Prostate Cancer


title: PR0763 Prostate Cancer


title: PR0753 Prostate Cancer


title: PR0762 Prostate Cancer


title: PR0755 Prostate Cancer


title: PR0745 Prostate Cancer


title: PR0744 Prostate Cancer


title: PR0740 Prostate Cancer


title: PR0742 Prostate Cancer


title: PR0749 Prostate Cancer


title: PR0743 Prostate Cancer


title: PR0735 Prostate Cancer


title: PR0737 Prostate Cancer


title: PR0739 Prostate Cancer


title: PR0730 Prostate Cancer


title: PR0729 Prostate Cancer


title: PR0731 Prostate Cancer


title: PR0734 Prostate Cancer


title: PR0727 Prostate Cancer


title: PR0726 Prostate Cancer


title: PR0725 Prostate Cancer


title: PR0724 Prostate Cancer


title: PR0723 Prostate Cancer


title: PR0728 Prostate Cancer


title: PR0771 Prostate Cancer


title: PR0722 Prostate Cancer


title: PR0721 Prostate Cancer


title: PR0738 Prostate Cancer


title: PR0719 Prostate Cancer


title: PR0736 Prostate Cancer


title: PR0713 Prostate Cancer


title: PR0716 Prostate Cancer


title: PR0715 Prostate Cancer


title: PR0712 Prostate Cancer


title: PR0710 Prostate Cancer


title: PR0760 Prostate Cancer


title: PR0720 Prostate Cancer


title: PR0708 Prostate Cancer


title: PR0707 Prostate Cancer


title: PR0709 Prostate Cancer


title: PR0703 Prostate Cancer


title: PR0717 Prostate Cancer


title: PR0705 Prostate Cancer


title: PR0706 Prostate Cancer


title: PR0718 Prostate Cancer


title: PR0702 Prostate Cancer


title: PR0695 Prostate Cancer


title: PR0704 Prostate Cancer


title: PR0701 Prostate Cancer


title: PR0697 Prostate Cancer


title: PR0714 Prostate Cancer


title: PR0693 Prostate Cancer


title: PR0699 Prostate Cancer


title: PR0700 Prostate Cancer


title: PR0689 Prostate Cancer


title: PR0711 Prostate Cancer


title: PR0690 Prostate Cancer


title: PR0694 Prostate Cancer


title: PR0692 Prostate Cancer


title: PR0685 Prostate Cancer


title: PR0691 Prostate Cancer


title: PR0687 Prostate Cancer


title: PR0676 Prostate Cancer


title: PR0679 Prostate Cancer


title: PR0681 Prostate Cancer


title: PR0682 Prostate Cancer


title: PR0678 Prostate Cancer


title: PR0675 Prostate Cancer


title: PR0671 Prostate Cancer


title: PR0677 Prostate Cancer


title: PR0674 Prostate Cancer


title: PR0672 Prostate Cancer


title: PR0652 Prostate Cancer


title: PR0658 Prostate Cancer


title: PR0670 Prostate Cancer


title: PR0662 Prostate Cancer


title: PR0648 Prostate Cancer


title: PR0805 Prostate Cancer


title: PR0668 Prostate Cancer


title: PR0643 Prostate Cancer


title: PR0669 Prostate Cancer


title: PR0660 Prostate Cancer


title: PR0659 Prostate Cancer


title: PR0667 Prostate Cancer


title: PR0640 Prostate Cancer


title: PR0665 Prostate Cancer


title: PR0664 Prostate Cancer


title: PR0650 Prostate Cancer


title: PR0651 Prostate Cancer


title: PR0639 Prostate Cancer


title: PR0642 Prostate Cancer


title: PR0653 Prostate Cancer


title: PR0637 Prostate Cancer


title: PR0641 Prostate Cancer


title: PR0645 Prostate Cancer


title: PR0638 Prostate Cancer


title: PR0636 Prostate Cancer


title: PR0646 Prostate Cancer


title: PR0633 Prostate Cancer


title: PR0632 Prostate Cancer


title: PR0634 Prostate Cancer


title: PR0631 Prostate Cancer


title: PR0786 Prostate Cancer


title: PR0635 Prostate Cancer


title: PR0783 Prostate Cancer


title: PR0630 Prostate Cancer


title: PR0619 Prostate Cancer


title: PR0615 Prostate Cancer


title: PR0612 Prostate Cancer


title: PR0610 Prostate Cancer


title: PR0602 Prostate Cancer


title: PR0601 Prostate Cancer


title: PR0605 Prostate Cancer


title: PR0618 Prostate Cancer


title: PR0609 Prostate Cancer


title: PR0606 Prostate Cancer


title: PR0604 Prostate Cancer


title: PR0627 Prostate Cancer


title: PR0596 Prostate Cancer


title: PR0598 Prostate Cancer


title: PR0595 Prostate Cancer


title: PR0594 Prostate Cancer


title: PR0624 Prostate Cancer


title: PR0621 Prostate Cancer


title: PR0589 Prostate Cancer


title: PR0586 Prostate Cancer


title: PR0581 Prostate Cancer


title: PR0628 Prostate Cancer


title: PR0611 Prostate Cancer


title: PR0593 Prostate Cancer


title: PR0591 Prostate Cancer


title: PR0580 Prostate Cancer


title: PR0578 Prostate Cancer


title: PR0584 Prostate Cancer


title: PR0577 Prostate Cancer


title: PR0576 Prostate Cancer


title: PR0573 Prostate Cancer


title: PR0575 Prostate Cancer


title: PR0608 Prostate Cancer


title: PR0571 Prostate Cancer


title: PR0569 Prostate Cancer


title: PR0566 Prostate Cancer


title: PR0567 Prostate Cancer


title: PR0565 Prostate Cancer


title: PR0564 Prostate Cancer


title: PR0570 Prostate Cancer


title: PR0563 Prostate Cancer


title: PR0559 Prostate Cancer


title: PR0557 Prostate Cancer


title: PR0555 Prostate Cancer


title: PR0549 Prostate Cancer


title: PR0552 Prostate Cancer


title: PR0554 Prostate Cancer


title: PR0551 Prostate Cancer


title: PR0553 Prostate Cancer


title: PR0550 Prostate Cancer


title: PR0543 Prostate Cancer


title: PR0544 Prostate Cancer


title: PR0545 Prostate Cancer


title: PR0546 Prostate Cancer


title: PR0547 Prostate Cancer


title: PR0541 Prostate Cancer


title: PR0562 Prostate Cancer


title: PR0540 Prostate Cancer


title: PR0539 Prostate Cancer


title: PR0538 Prostate Cancer


title: PR0537 Prostate Cancer


title: PR0561 Prostate Cancer


title: PR0556 Prostate Cancer


title: PR0535 Prostate Cancer


title: PR0532 Prostate Cancer


title: PR0530 Prostate Cancer


title: PR0542 Prostate Cancer


title: PR0531 Prostate Cancer


title: PR0536 Prostate Cancer


title: PR0529 Prostate Cancer


title: PR0528 Prostate Cancer


title: PR0526 Prostate Cancer


title: PR0527 Prostate Cancer


title: PR0522 Prostate Cancer


title: PR0524 Prostate Cancer


title: PR0516 Prostate Cancer


title: PR0517 Prostate Cancer


title: PR0513 Prostate Cancer


title: PR0519 Prostate Cancer


title: PR0512 Prostate Cancer


title: PR0520 Prostate Cancer


title: PR0525 Prostate Cancer


title: PR0515 Prostate Cancer


title: PR0509 Prostate Cancer


title: PR0533 Prostate Cancer


title: PR0508 Prostate Cancer


title: PR0506 Prostate Cancer


title: PR0507 Prostate Cancer


title: PR0504 Prostate Cancer


title: PR0505 Prostate Cancer


title: PR0501 Prostate Cancer


title: PR0502 Prostate Cancer


title: PR0510 Prostate Cancer


title: PR0499 Prostate Cancer


title: PR0500 Prostate Cancer


title: PR0498 Prostate Cancer


title: PR0521 Prostate Cancer


title: PR0511 Prostate Cancer


title: PR0491 Prostate Cancer


title: PR0490 Prostate Cancer


title: PR0486 Prostate Cancer


title: PR0489 Prostate Cancer


title: PR0495 Prostate Cancer


title: PR0485 Prostate Cancer


title: PR0488 Prostate Cancer


title: PR0477 Prostate Cancer


title: PR0476 Prostate Cancer


title: PR0478 Prostate Cancer


title: PR0480 Prostate Cancer


title: PR0479 Prostate Cancer


title: PR0481 Prostate Cancer


title: PR0475 Prostate Cancer


title: PR0472 Prostate Cancer


title: PR0474 Prostate Cancer


title: PR0469 Prostate Cancer


title: PR0482 Prostate Cancer


title: PR0468 Prostate Cancer


title: PR0473 Prostate Cancer


title: PR0467 Prostate Cancer


title: PR0465 Prostate Cancer


title: PR0493 Prostate Cancer


title: PR0462 Prostate Cancer


title: PR0463 Prostate Cancer


title: PR0461 Prostate Cancer


title: PR0460 Prostate Cancer


title: PR0459 Prostate Cancer


title: PR0458 Prostate Cancer


title: PR0457 Prostate Cancer


title: PR0456 Prostate Cancer


title: PR0455 Prostate Cancer


title: PR0446 Prostate Cancer


title: PR0447 Prostate Cancer


title: PR0449 Prostate Cancer


title: PR0448 Prostate Cancer


title: PR0451 Prostate Cancer


title: PR0432 Prostate Cancer


title: PR0429 Prostate Cancer


title: PR0443 Prostate Cancer


title: PR0444 Prostate Cancer


title: PR0440 Prostate Cancer


title: PR0434 Prostate Cancer


title: PR0437 Prostate Cancer


title: PR0442 Prostate Cancer


title: PR0436 Prostate Cancer


title: PR0425 Prostate Cancer


title: PR0427 Prostate Cancer


title: PR0431 Prostate Cancer


title: PR0428 Prostate Cancer


title: PR0450 Prostate Cancer


title: PR0419 Prostate Cancer


title: PR0454 Prostate Cancer


title: PR0422 Prostate Cancer


title: PR0420 Prostate Cancer


title: PR0417 Prostate Cancer


title: PR0439 Prostate Cancer


title: PR0433 Prostate Cancer


title: PR0416 Prostate Cancer


title: PR0415 Prostate Cancer


title: PR0410 Prostate Cancer


title: PR0403 Prostate Cancer


title: PR0423 Prostate Cancer


title: PR0404 Prostate Cancer


title: PR0401 Prostate Cancer


title: PR0412 Prostate Cancer


title: PR0402 Prostate Cancer


title: PR0407 Prostate Cancer


title: PR0386 Prostate Cancer


title: PR0389 Prostate Cancer


title: PR0397 Prostate Cancer


title: PR0391 Prostate Cancer


title: PR0385 Prostate Cancer


title: PR0382 Prostate Cancer


title: PR0390 Prostate Cancer


title: PR0395 Prostate Cancer


title: PR0383 Prostate Cancer


title: PR0381 Prostate Cancer


title: PR0379 Prostate Cancer


title: PR0411 Prostate Cancer


title: PR0409 Prostate Cancer


title: PR0399 Prostate Cancer


title: PR0376 Prostate Cancer


title: PR0377 Prostate Cancer


title: PR0398 Prostate Cancer


title: PR0375 Prostate Cancer


title: PR0374 Prostate Cancer


title: PR0387 Prostate Cancer


title: PR0396 Prostate Cancer


title: PR0380 Prostate Cancer


title: PR0365 Prostate Cancer


title: PR0368 Prostate Cancer


title: PR0372 Prostate Cancer


title: PR0364 Prostate Cancer


title: PR0367 Prostate Cancer


title: PR0363 Prostate Cancer


title: PR0362 Prostate Cancer


title: PR0369 Prostate Cancer


title: PR0360 Prostate Cancer


title: PR0358 Prostate Cancer


title: PR0357 Prostate Cancer


title: PR0356 Prostate Cancer


title: PR0354 Prostate Cancer


title: PR0359 Prostate Cancer


title: PR0361 Prostate Cancer


title: PR0353 Prostate Cancer


title: PR0351 Prostate Cancer


title: PR0350 Prostate Cancer


title: PR0352 Prostate Cancer


title: PR0349 Prostate Cancer


title: PR0343 Prostate Cancer


title: PR0346 Prostate Cancer


title: PR0348 Prostate Cancer


title: PR0347 Prostate Cancer


title: PR0341 Prostate Cancer


title: PR0338 Prostate Cancer


title: PR0336 Prostate Cancer


title: PR0335 Prostate Cancer


title: PR0334 Prostate Cancer


title: PR0329 Prostate Cancer


title: PR0332 Prostate Cancer


title: PR0333 Prostate Cancer


title: PR0331 Prostate Cancer


title: PR0328 Prostate Cancer


title: PR0326 Prostate Cancer


title: PR0325 Prostate Cancer


title: PR0317 Prostate Cancer


title: PR0319 Prostate Cancer


title: PR0327 Prostate Cancer


title: PR0323 Prostate Cancer


title: PR0321 Prostate Cancer


title: PR0316 Prostate Cancer


title: PR0322 Prostate Cancer


title: PR0318 Prostate Cancer


title: PR0330 Prostate Cancer


title: PR0320 Prostate Cancer


title: PR0312 Prostate Cancer


title: PR0313 Prostate Cancer


title: PR0310 Prostate Cancer


title: PR0309 Prostate Cancer


title: PR0305 Prostate Cancer


title: PR0303 Prostate Cancer


title: PR0300 Prostate Cancer


title: PR0302 Prostate Cancer


title: PR0299 Prostate Cancer


title: PR0308 Prostate Cancer


title: PR0296 Prostate Cancer


title: PR0298 Prostate Cancer


title: PR0294 Prostate Cancer


title: PR0311 Prostate Cancer


title: PR0295 Prostate Cancer


title: PR0304 Prostate Cancer


title: PR0290 Prostate Cancer


title: PR0289 Prostate Cancer


title: PR0277 Prostate Cancer


title: PR0286 Prostate Cancer


title: PR0301 Prostate Cancer


title: PR0291 Prostate Cancer


title: PR0292 Prostate Cancer


title: PR0282 Prostate Cancer


title: PR0278 Prostate Cancer


title: PR0283 Prostate Cancer


title: PR0281 Prostate Cancer


title: PR0272 Prostate Cancer


title: PR0284 Prostate Cancer


title: PR0279 Prostate Cancer


title: PR0274 Prostate Cancer


title: PR0275 Prostate Cancer


title: PR0273 Prostate Cancer


title: PR0293 Prostate Cancer


title: PR0262 Prostate Cancer


title: PR0267 Prostate Cancer


title: PR0271 Prostate Cancer


title: PR0266 Prostate Cancer


title: PR0270 Prostate Cancer


title: PR0268 Prostate Cancer


title: PR0265 Prostate Cancer


title: PR0264 Prostate Cancer


title: PR0263 Prostate Cancer


title: PR0260 Prostate Cancer


title: PR0280 Prostate Cancer


title: PR0258 Prostate Cancer


title: PR0257 Prostate Cancer


title: PR0253 Prostate Cancer


title: PR0255 Prostate Cancer


title: PR0256 Prostate Cancer


title: PR0254 Prostate Cancer


title: PR0241 Prostate Cancer


title: PR0261 Prostate Cancer


title: PR0243 Prostate Cancer


title: PR0251 Prostate Cancer


title: PR0250 Prostate Cancer


title: PR0245 Prostate Cancer


title: PR0247 Prostate Cancer


title: PR0246 Prostate Cancer


title: PR0252 Prostate Cancer


title: PR0249 Prostate Cancer


title: PR0244 Prostate Cancer


title: PR0240 Prostate Cancer


title: PR0238 Prostate Cancer


title: PR0237 Prostate Cancer


title: PR0236 Prostate Cancer


title: PR0232 Prostate Cancer


title: PR0239 Prostate Cancer


title: PR0259 Prostate Cancer


title: PR0233 Prostate Cancer


title: PR0231 Prostate Cancer


title: PR0230 Prostate Cancer


title: PR0229 Prostate Cancer


title: PR0228 Prostate Cancer


title: PR0227 Prostate Cancer


title: PR0224 Prostate Cancer


title: PR0222 Prostate Cancer


title: PR0225 Prostate Cancer


title: PR0221 Prostate Cancer


title: PR0219 Prostate Cancer


title: PR0218 Prostate Cancer


title: PR0217 Prostate Cancer


title: PR0223 Prostate Cancer


title: PR0209 Prostate Cancer


title: PR0212 Prostate Cancer


title: PR0220 Prostate Cancer


title: PR0210 Prostate Cancer


title: PR0215 Prostate Cancer


title: PR0216 Prostate Cancer


title: PR0214 Prostate Cancer


title: PR0213 Prostate Cancer


title: PR0206 Prostate Cancer


title: PR0208 Prostate Cancer


title: PR0205 Prostate Cancer


title: PR0207 Prostate Cancer


title: PR0203 Prostate Cancer


title: PR0201 Prostate Cancer


title: PR0211 Prostate Cancer


title: PR0202 Prostate Cancer


title: PR0195 Prostate Cancer


title: PR0190 Prostate Cancer


title: PR0187 Prostate Cancer


title: PR0188 Prostate Cancer


title: PR0194 Prostate Cancer


title: PR0189 Prostate Cancer


title: PR0186 Prostate Cancer


title: PR0193 Prostate Cancer


title: PR0184 Prostate Cancer


title: PR0196 Prostate Cancer


title: PR0183 Prostate Cancer


title: PR0166 Prostate Cancer


title: PR0181 Prostate Cancer


title: PR0173 Prostate Cancer


title: PR0172 Prostate Cancer


title: PR0177 Prostate Cancer


title: PR0180 Prostate Cancer


title: PR0178 Prostate Cancer


title: PR0176 Prostate Cancer


title: PR0171 Prostate Cancer


title: PR0175 Prostate Cancer


title: PR0170 Prostate Cancer


title: PR0168 Prostate Cancer


title: PR0200 Prostate Cancer


title: PR0182 Prostate Cancer


title: PR0167 Prostate Cancer


title: PR0199 Prostate Cancer


title: PR0164 Prostate Cancer


title: PR0163 Prostate Cancer


title: PR0165 Prostate Cancer


title: PR0174 Prostate Cancer


title: PR0158 Prostate Cancer


title: PR0159 Prostate Cancer


title: PR0162 Prostate Cancer


title: PR0156 Prostate Cancer


title: PR0155 Prostate Cancer


title: PR0157 Prostate Cancer


title: PR0144 Prostate Cancer


title: PR0142 Prostate Cancer


title: PR0137 Prostate Cancer


title: PR0143 Prostate Cancer


title: PR0141 Prostate Cancer


title: PR0147 Prostate Cancer


title: PR0140 Prostate Cancer


title: PR0148 Prostate Cancer


title: PR0160 Prostate Cancer


title: PR0138 Prostate Cancer


title: PR0150 Prostate Cancer


title: PR0152 Prostate Cancer


title: PR0161 Prostate Cancer


title: PR0136 Prostate Cancer


title: PR0153 Prostate Cancer


title: PR0149 Prostate Cancer


title: PR0134 Prostate Cancer


title: PR0133 Prostate Cancer


title: PR0151 Prostate Cancer


title: PR0154 Prostate Cancer


title: PR0130 Prostate Cancer


title: PR0129 Prostate Cancer


title: PR0125 Prostate Cancer


title: PR0126 Prostate Cancer


title: PR0145 Prostate Cancer


title: PR0135 Prostate Cancer


title: PR0128 Prostate Cancer


title: PR0132 Prostate Cancer


title: PR0124 Prostate Cancer


title: PR0123 Prostate Cancer


title: PR0119 Prostate Cancer


title: PR0122 Prostate Cancer


title: PR0121 Prostate Cancer


title: PR0106 Prostate Cancer


title: PR0115 Prostate Cancer


title: PR0107 Prostate Cancer


title: PR0111 Prostate Cancer


title: PR0100 Prostate Cancer


title: PR0108 Prostate Cancer


title: PR0127 Prostate Cancer


title: PR0102 Prostate Cancer


title: PR0104 Prostate Cancer


title: PR0099 Prostate Cancer


title: PR0101 Prostate Cancer


title: PR0113 Prostate Cancer


title: PR0098 Prostate Cancer


title: PR0097 Prostate Cancer


title: PR0096 Prostate Cancer


title: PR0105 Prostate Cancer


title: PR0088 Prostate Cancer


title: PR0087 Prostate Cancer


title: PR0090 Prostate Cancer


title: PR0089 Prostate Cancer


title: PR0091 Prostate Cancer


title: PR0094 Prostate Cancer


title: PR0103 Prostate Cancer


title: PR0086 Prostate Cancer


title: PR0110 Prostate Cancer


title: PR0085 Prostate Cancer


title: PR0081 Prostate Cancer


title: PR0084 Prostate Cancer


title: PR0083 Prostate Cancer


title: PR0079 Prostate Cancer


title: PR0078 Prostate Cancer


title: PR0080 Prostate Cancer


title: PR0068 Prostate Cancer


title: PR0077 Prostate Cancer


title: PR0075 Prostate Cancer


title: PR0076 Prostate Cancer


title: PR0071 Prostate Cancer


title: PR0072 Prostate Cancer


title: PR0073 Prostate Cancer


title: PR0074 Prostate Cancer


title: PR0070 Prostate Cancer


title: PR0065 Prostate Cancer


title: PR0067 Prostate Cancer


title: PR0066 Prostate Cancer


title: PR0059 Prostate Cancer


title: PR0062 Prostate Cancer


title: PR0061 Prostate Cancer


title: PR0058 Prostate Cancer


title: PR0056 Prostate Cancer


title: PR0069 Prostate Cancer


title: PR0064 Prostate Cancer


title: PR0060 Prostate Cancer


title: PR0063 Prostate Cancer


title: PR0053 Prostate Cancer


title: PR0049 Prostate Cancer


title: PR0048 Prostate Cancer


title: PR0050 Prostate Cancer


title: PR0047 Prostate Cancer


title: PR0054 Prostate Cancer


title: PR0057 Prostate Cancer


title: PR0036 Prostate Cancer


title: PR0039 Prostate Cancer


title: PR0037 Prostate Cancer


title: PR0046 Prostate Cancer


title: PR0040 Prostate Cancer


title: PR0055 Prostate Cancer


title: PR0043 Prostate Cancer


title: PR0038 Prostate Cancer


title: PR0041 Prostate Cancer


title: PR0052 Prostate Cancer


title: PR0033 Prostate Cancer


title: PR0034 Prostate Cancer


title: PR0035 Prostate Cancer


title: PR0051 Prostate Cancer


title: PR0025 Prostate Cancer


title: PR0027 Prostate Cancer


title: PR0032 Prostate Cancer


title: PR0026 Prostate Cancer


title: PR0028 Prostate Cancer


title: PR0031 Prostate Cancer


title: PR0030 Prostate Cancer


title: PR0042 Prostate Cancer


title: PR0024 Prostate Cancer


title: PR0021 Prostate Cancer


title: PR0019 Prostate Cancer


title: PR0018 Prostate Cancer


title: PR0017 Prostate Cancer


title: PR0016 Prostate Cancer


title: PR0009 Prostate Cancer


title: PR0007 Prostate Cancer


title: PR0004 Prostate Cancer


title: PR0005 Prostate Cancer


title: PR0002 Prostate Cancer


title: PR0008 Prostate Cancer


title: PR0003 Prostate Cancer


title: PR0015 Prostate Cancer


title: PR0013 Prostate Cancer


title: PC0848 Pancreatic Cancer

value: Pancreatic Cancer


title: PR0001 Prostate Cancer


title: PR0023 Prostate Cancer


title: PR0022 Prostate Cancer


title: PC0806 Pancreatic Cancer


title: PR0020 Prostate Cancer


title: PC0634 Pancreatic Cancer


title: PC0706 Pancreatic Cancer


title: PC0764 Pancreatic Cancer


title: PC0669 Pancreatic Cancer


title: PR0092 Prostate Cancer


title: PC0714 Pancreatic Cancer


title: PC0591 Pancreatic Cancer


title: PR0006 Prostate Cancer


title: PC0543 Pancreatic Cancer


title: PC0647 Pancreatic Cancer


title: PC0801 Pancreatic Cancer


title: PC0670 Pancreatic Cancer


title: PC0588 Pancreatic Cancer


title: PC0544 Pancreatic Cancer


title: PC0512 Pancreatic Cancer


title: PC0524 Pancreatic Cancer


title: PC0493 Pancreatic Cancer


title: PC0447 Pancreatic Cancer


title: PC0418 Pancreatic Cancer


title: PC0460 Pancreatic Cancer


title: PC0409 Pancreatic Cancer


title: PC0408 Pancreatic Cancer


title: PC0403 Pancreatic Cancer


title: PC0456 Pancreatic Cancer


title: PC0397 Pancreatic Cancer


title: PC0387 Pancreatic Cancer


title: PC0618 Pancreatic Cancer


title: PC0350 Pancreatic Cancer


title: PC0352 Pancreatic Cancer


title: PC0344 Pancreatic Cancer


title: PC0324 Pancreatic Cancer


title: PC0291 Pancreatic Cancer


title: PC0302 Pancreatic Cancer


title: PC0333 Pancreatic Cancer


title: PC0284 Pancreatic Cancer


title: PC0225 Pancreatic Cancer


title: PC0235 Pancreatic Cancer


title: PC0059 Pancreatic Cancer


title: PC0167 Pancreatic Cancer


title: PC0223 Pancreatic Cancer


title: PC0076 Pancreatic Cancer


title: PC0196 Pancreatic Cancer


title: PC0164 Pancreatic Cancer


title: PC0133 Pancreatic Cancer


title: XB0969 non-Cancer

value: non-Cancer


title: XB0925 non-Cancer


title: PC0115 Pancreatic Cancer


title: PC0130 Pancreatic Cancer


title: PC0088 Pancreatic Cancer


title: PC0085 Pancreatic Cancer


title: PC0026 Pancreatic Cancer


title: XB0832 non-Cancer


title: XB0666 non-Cancer


title: XB0923 non-Cancer


title: XB0773 non-Cancer


title: XB0637 non-Cancer


title: XB0653 non-Cancer


title: XB0656 non-Cancer


title: PC0112 Pancreatic Cancer


title: XB0629 non-Cancer


title: XB0620 non-Cancer


title: XB0574 non-Cancer


title: XB0833 non-Cancer


title: XB0414 non-Cancer


title: XB0403 non-Cancer


title: XB0347 non-Cancer


title: XB0284 non-Cancer


title: NB14051208 non-Cancer


title: NB14050201 non-Cancer


title: NB13120904 non-Cancer


title: NB14051207 non-Cancer


title: NB14050703 non-Cancer


title: NB14020503 non-Cancer


title: NB13112003 non-Cancer


title: XB0453 non-Cancer


title: NB13082605 non-Cancer


title: NB12111604 non-Cancer


title: NB12072701 non-Cancer


title: NB12091403 non-Cancer


title: NB12112003 non-Cancer


title: NB12081301 non-Cancer


title: NB13010802 non-Cancer


title: M12012302 non-Cancer


title: NB12022205 non-Cancer


title: NB13070807 non-Cancer


title: NB12040304 non-Cancer


title: M11053103 non-Cancer


title: M11031802 non-Cancer


title: M11051803 non-Cancer


title: PR1285 Negative prostate biopsy

value: Negative prostate biopsy


title: CHC895 non-Cancer


title: M10121402 non-Cancer


title: PR1284 Negative prostate biopsy


title: PR1282 Negative prostate biopsy


title: PR1280 Negative prostate biopsy


title: PR1275 Negative prostate biopsy


title: PR1278 Negative prostate biopsy


title: PR1274 Negative prostate biopsy


title: PR1276 Negative prostate biopsy


title: PR1277 Negative prostate biopsy


title: PR1279 Negative prostate biopsy


title: PR1266 Negative prostate biopsy


title: PR1281 Negative prostate biopsy


title: PR1272 Negative prostate biopsy


title: PR1268 Negative prostate biopsy


title: PR1269 Negative prostate biopsy


title: PR1265 Negative prostate biopsy


title: PR1261 Negative prostate biopsy


title: PR1267 Negative prostate biopsy


title: PR1259 Negative prostate biopsy


title: PR1262 Negative prostate biopsy


title: PR1271 Negative prostate biopsy


title: PR1270 Negative prostate biopsy


title: PR1260 Negative prostate biopsy


title: PR1263 Negative prostate biopsy


title: PR1264 Negative prostate biopsy


title: PR1273 Negative prostate biopsy


title: PR1258 Negative prostate biopsy


title: PR1257 Negative prostate biopsy


title: PR1256 Negative prostate biopsy


title: PR1255 Negative prostate biopsy


title: PR1254 Negative prostate biopsy


title: PR1253 Negative prostate biopsy


title: PR1249 Negative prostate biopsy


title: PR1250 Negative prostate biopsy


title: PR1251 Negative prostate biopsy


title: PR1246 Negative prostate biopsy


title: PR1247 Negative prostate biopsy


title: PR1252 Negative prostate biopsy


title: PR1238 Negative prostate biopsy


title: PR1248 Negative prostate biopsy


title: PR1239 Negative prostate biopsy


title: PR1240 Negative prostate biopsy


title: PR1236 Negative prostate biopsy


title: PR1245 Negative prostate biopsy


title: PR1243 Negative prostate biopsy


title: PR1244 Negative prostate biopsy


title: PR1241 Negative prostate biopsy


title: PR1242 Negative prostate biopsy


title: PR1237 Negative prostate biopsy


title: PR1231 Negative prostate biopsy


title: PR1234 Negative prostate biopsy


title: PR1235 Negative prostate biopsy


title: PR1233 Negative prostate biopsy


title: PR1230 Negative prostate biopsy


title: PR1228 Negative prostate biopsy


title: PR1232 Negative prostate biopsy


title: PR1225 Negative prostate biopsy


title: PR1229 Negative prostate biopsy


title: PR1226 Negative prostate biopsy


title: PR1227 Negative prostate biopsy


title: PR1203 Negative prostate biopsy


title: PR1205 Negative prostate biopsy


title: PR1206 Negative prostate biopsy


title: PR1202 Negative prostate biopsy


title: PR1204 Negative prostate biopsy


title: PR1217 Negative prostate biopsy


title: PR1216 Negative prostate biopsy


title: PR1219 Negative prostate biopsy


title: PR1209 Negative prostate biopsy


title: PR1220 Negative prostate biopsy


title: PR1207 Negative prostate biopsy


title: PR1208 Negative prostate biopsy


title: PR1224 Negative prostate biopsy


title: PR1215 Negative prostate biopsy


title: PR1222 Negative prostate biopsy


title: PR1211 Negative prostate biopsy


title: PR1223 Negative prostate biopsy


title: PR1218 Negative prostate biopsy


title: PR1210 Negative prostate biopsy


title: PR1213 Negative prostate biopsy


title: PR1221 Negative prostate biopsy


title: PR1214 Negative prostate biopsy


title: PR1200 Negative prostate biopsy


title: PR1201 Negative prostate biopsy


title: PR1196 Negative prostate biopsy


title: PR1199 Negative prostate biopsy


title: PR1194 Negative prostate biopsy


title: PR1195 Negative prostate biopsy


title: PR1197 Negative prostate biopsy


title: PR1198 Negative prostate biopsy


title: PR1193 Negative prostate biopsy


title: PR1187 Negative prostate biopsy


title: PR1192 Negative prostate biopsy


title: PR1188 Negative prostate biopsy


title: PR1185 Negative prostate biopsy


title: PR1189 Negative prostate biopsy


title: PR1179 Negative prostate biopsy


title: PR1177 Negative prostate biopsy


title: PR1212 Negative prostate biopsy


title: PR1176 Negative prostate biopsy


title: PR1174 Negative prostate biopsy


title: PR1186 Negative prostate biopsy


title: PR1172 Negative prostate biopsy


title: PR1191 Negative prostate biopsy


title: PR1175 Negative prostate biopsy


title: PR1183 Negative prostate biopsy


title: PR1190 Negative prostate biopsy


title: PR1173 Negative prostate biopsy


title: PR1181 Negative prostate biopsy


title: PR1182 Negative prostate biopsy


title: PR1180 Negative prostate biopsy


title: PR1171 Negative prostate biopsy


title: PR1184 Negative prostate biopsy


title: PR1168 Negative prostate biopsy


title: PR1170 Negative prostate biopsy


title: PR1166 Negative prostate biopsy


title: PR1169 Negative prostate biopsy


title: PR1167 Negative prostate biopsy


title: PR1178 Negative prostate biopsy


title: PR1165 Negative prostate biopsy


title: PR1163 Negative prostate biopsy


title: PR1164 Negative prostate biopsy


title: PR1160 Negative prostate biopsy


title: PR1162 Negative prostate biopsy


title: PR1161 Negative prostate biopsy


title: PR1156 Negative prostate biopsy


title: PR1158 Negative prostate biopsy


title: PR1157 Negative prostate biopsy


title: PR1159 Negative prostate biopsy


title: PR1145 Negative prostate biopsy


title: PR1148 Negative prostate biopsy


title: PR1155 Negative prostate biopsy


title: PR1154 Negative prostate biopsy


title: PR1151 Negative prostate biopsy


title: PR1152 Negative prostate biopsy


title: PR1153 Negative prostate biopsy


title: PR1150 Negative prostate biopsy


title: PR1146 Negative prostate biopsy


title: PR1149 Negative prostate biopsy


title: PR1283 Negative prostate biopsy


title: PR1141 Negative prostate biopsy


title: PR1147 Negative prostate biopsy


title: PR1142 Negative prostate biopsy


title: PR1143 Negative prostate biopsy


title: PR1140 Negative prostate biopsy


title: PR1139 Negative prostate biopsy


title: PR1138 Negative prostate biopsy


title: PR1130 Negative prostate biopsy


title: PR1131 Negative prostate biopsy


title: PR1128 Negative prostate biopsy


title: PR1129 Negative prostate biopsy


title: PR1144 Negative prostate biopsy


title: PR1135 Negative prostate biopsy


title: PR1136 Negative prostate biopsy


title: PR1133 Negative prostate biopsy


title: PR1134 Negative prostate biopsy


title: PR1127 Negative prostate biopsy


title: PR1125 Negative prostate biopsy


title: PR1126 Negative prostate biopsy


title: PR1124 Negative prostate biopsy


title: PR1137 Negative prostate biopsy


title: PR1123 Negative prostate biopsy


title: PR1121 Negative prostate biopsy


title: PR1122 Negative prostate biopsy


title: PR1119 Negative prostate biopsy


title: PR1120 Negative prostate biopsy


title: PR1118 Negative prostate biopsy


title: PR1132 Negative prostate biopsy


title: PR1112 Negative prostate biopsy


title: PR1114 Negative prostate biopsy


title: PR1116 Negative prostate biopsy


title: PR1115 Negative prostate biopsy


title: PR1117 Negative prostate biopsy


title: PR1111 Negative prostate biopsy


title: PR1113 Negative prostate biopsy


title: PR1103 Negative prostate biopsy


title: PR1102 Negative prostate biopsy


title: PR1108 Negative prostate biopsy


title: PR1104 Negative prostate biopsy


title: PR1101 Negative prostate biopsy


title: PR1106 Negative prostate biopsy


title: PR1100 Negative prostate biopsy


title: PR1105 Negative prostate biopsy


title: PR1098 Negative prostate biopsy


title: PR1097 Negative prostate biopsy


title: PR1099 Negative prostate biopsy


title: PR1107 Negative prostate biopsy


title: PR1110 Negative prostate biopsy


title: PR1091 Negative prostate biopsy


title: PR1094 Negative prostate biopsy


title: PR1109 Negative prostate biopsy


title: PR1095 Negative prostate biopsy


title: PR1093 Negative prostate biopsy


title: PR1090 Negative prostate biopsy


title: PR1088 Negative prostate biopsy


title: PR1096 Negative prostate biopsy


title: PR1086 Negative prostate biopsy


title: PR1082 Negative prostate biopsy


title: PR1083 Negative prostate biopsy


title: PR1087 Negative prostate biopsy


title: PR1084 Negative prostate biopsy


title: PR1085 Negative prostate biopsy


title: PR1092 Negative prostate biopsy


title: PR1080 Negative prostate biopsy


title: PR1089 Negative prostate biopsy


title: PR1077 Negative prostate biopsy


title: PR1075 Negative prostate biopsy


title: PR1078 Negative prostate biopsy


title: PR1076 Negative prostate biopsy


title: PR1069 Negative prostate biopsy


title: PR1070 Negative prostate biopsy


title: PR1073 Negative prostate biopsy


title: PR1071 Negative prostate biopsy


title: PR1074 Negative prostate biopsy


title: PR1081 Negative prostate biopsy


title: PR1067 Negative prostate biopsy


title: PR1068 Negative prostate biopsy


title: PR1059 Negative prostate biopsy


title: PR1065 Negative prostate biopsy


title: PR1064 Negative prostate biopsy


title: PR1060 Negative prostate biopsy


title: PR1062 Negative prostate biopsy


title: PR1063 Negative prostate biopsy


title: PR1061 Negative prostate biopsy


title: PR1072 Negative prostate biopsy


title: PR1058 Negative prostate biopsy


title: PR1057 Negative prostate biopsy


title: PR1056 Negative prostate biopsy


title: PR1079 Negative prostate biopsy


title: PR1055 Negative prostate biopsy


title: PR1052 Negative prostate biopsy


title: PR1053 Negative prostate biopsy


title: PR1051 Negative prostate biopsy


title: PR1066 Negative prostate biopsy


title: PR1050 Negative prostate biopsy


title: PR1046 Negative prostate biopsy


title: PR1049 Negative prostate biopsy


title: PR1048 Negative prostate biopsy


title: LK1700 Lung Cancer

value: Lung Cancer


title: LK1714 Lung Cancer


title: LK1660 Lung Cancer


title: LK1478 Lung Cancer


title: LK1633 Lung Cancer


title: LK1585 Lung Cancer


title: LK1570 Lung Cancer


title: PR1054 Negative prostate biopsy


title: LK1493 Lung Cancer


title: LK1550 Lung Cancer


title: LK1462 Lung Cancer


title: PR1047 Negative prostate biopsy


title: LK1428 Lung Cancer


title: LK1419 Lung Cancer


title: LK1464 Lung Cancer


title: LK1308 Lung Cancer


title: LK1327 Lung Cancer


title: LK1190 Lung Cancer


title: LK1121 Lung Cancer


title: LK1649 Lung Cancer


title: LK1693 Lung Cancer


title: PR1045 Negative prostate biopsy


title: LK1105 Lung Cancer


title: LK1230 Lung Cancer


title: LK1172 Lung Cancer


title: LK1104 Lung Cancer


title: LK0583 Lung Cancer


title: LK0857 Lung Cancer


title: LK0841 Lung Cancer


title: LK0850 Lung Cancer


title: LK0794 Lung Cancer


title: LK0866 Lung Cancer


title: LK0931 Lung Cancer


title: LK0503 Lung Cancer


title: LK0442 Lung Cancer


title: LK0405 Lung Cancer


title: LK0399 Lung Cancer


title: LK1076 Lung Cancer


title: LK0649 Lung Cancer


title: LK0603 Lung Cancer


title: LK0630 Lung Cancer


title: LK0589 Lung Cancer


title: LK0398 Lung Cancer


title: LK0691 Lung Cancer


title: LK0347 Lung Cancer


title: LK0198 Lung Cancer


title: HC0356 Hepatocellular Carcinoma

value: Hepatocellular Carcinoma


title: HC0355 Hepatocellular Carcinoma


title: LK0944 Lung Cancer


title: LK0104 Lung Cancer


title: LK0158 Lung Cancer


title: LK0334 Lung Cancer


title: HC0319 Hepatocellular Carcinoma


title: HC0334 Hepatocellular Carcinoma


title: LK0041 Lung Cancer


title: LK0011 Lung Cancer


title: HC0354 Hepatocellular Carcinoma


title: LK0315 Lung Cancer


title: HC0351 Hepatocellular Carcinoma


title: HC0340 Hepatocellular Carcinoma


title: HC0282 Hepatocellular Carcinoma


title: HC0286 Hepatocellular Carcinoma


title: HC0244 Hepatocellular Carcinoma


title: HC0222 Hepatocellular Carcinoma


title: HC0331 Hepatocellular Carcinoma


title: HC0275 Hepatocellular Carcinoma


title: HC0198 Hepatocellular Carcinoma


title: HC0320 Hepatocellular Carcinoma


title: HC0283 Hepatocellular Carcinoma


title: HC0188 Hepatocellular Carcinoma


title: HC0204 Hepatocellular Carcinoma


title: HC0243 Hepatocellular Carcinoma


title: HC0347 Hepatocellular Carcinoma


title: HC0171 Hepatocellular Carcinoma


title: HC0176 Hepatocellular Carcinoma


title: HC0227 Hepatocellular Carcinoma


title: HC0178 Hepatocellular Carcinoma


title: HC0208 Hepatocellular Carcinoma


title: HC0240 Hepatocellular Carcinoma


title: HC0141 Hepatocellular Carcinoma


title: HC0131 Hepatocellular Carcinoma


title: HC0126 Hepatocellular Carcinoma


title: HC0097 Hepatocellular Carcinoma


title: HC0115 Hepatocellular Carcinoma


title: HC0109 Hepatocellular Carcinoma


title: HC0074 Hepatocellular Carcinoma


title: HC0065 Hepatocellular Carcinoma


title: HC0196 Hepatocellular Carcinoma


title: HC0150 Hepatocellular Carcinoma


title: HC0087 Hepatocellular Carcinoma


title: HC0059 Hepatocellular Carcinoma


title: HC0061 Hepatocellular Carcinoma


title: HC0089 Hepatocellular Carcinoma


title: HC0028 Hepatocellular Carcinoma


title: HC0042 Hepatocellular Carcinoma


title: HC0093 Hepatocellular Carcinoma


title: HC0228 Hepatocellular Carcinoma


title: HC0015 Hepatocellular Carcinoma


title: HC0183 Hepatocellular Carcinoma


title: HC0004 Hepatocellular Carcinoma


title: HC0009 Hepatocellular Carcinoma


title: GL0183 Glioma

value: Glioma


title: GL0216 Glioma


title: GL0174 Glioma


title: GL0188 Glioma


title: GL0179 Glioma


title: GL0210 Glioma


title: GL0204 Glioma


title: GL0176 Glioma


title: GL0168 Glioma


title: GL0194 Glioma


title: GL0206 Glioma


title: GL0198 Glioma


title: GL0158 Glioma


title: GL0150 Glioma


title: GL0159 Glioma


title: GL0140 Glioma


title: GL0149 Glioma


title: GL0126 Glioma


title: GL0130 Glioma


title: GL0145 Glioma


title: GL0114 Glioma


title: GL0124 Glioma


title: GL0117 Glioma


title: HC0020 Hepatocellular Carcinoma


title: GL0120 Glioma


title: GL0109 Glioma


title: GL0132 Glioma


title: GL0105 Glioma


title: GL0107 Glioma


title: GL0076 Glioma


title: GL0103 Glioma


title: GL0067 Glioma


title: GL0070 Glioma


title: GL0075 Glioma


title: GL0086 Glioma


title: GL0089 Glioma


title: GL0112 Glioma


title: GL0088 Glioma


title: GL0053 Glioma


title: GL0048 Glioma


title: GL0019 Glioma


title: GL0034 Glioma


title: GL0017 Glioma


title: GL0025 Glioma


title: GL0011 Glioma


title: GL0009 Glioma


title: GL0056 Glioma


title: GL0068 Glioma


title: GC1375 Gastric Cancer

value: Gastric Cancer


title: GC1464 Gastric Cancer


title: GC1300 Gastric Cancer


title: GC1153 Gastric Cancer


title: GC1183 Gastric Cancer


title: HC0213 Hepatocellular Carcinoma


title: GL0100 Glioma


title: GL0004 Glioma


title: GC0938 Gastric Cancer


title: GC0996 Gastric Cancer


title: GC1145 Gastric Cancer


title: GC0994 Gastric Cancer


title: GC1143 Gastric Cancer


title: GC0702 Gastric Cancer


title: GC0910 Gastric Cancer


title: GC0962 Gastric Cancer


title: GC0836 Gastric Cancer


title: GC0879 Gastric Cancer


title: GC0885 Gastric Cancer


title: GC0705 Gastric Cancer


title: GC0676 Gastric Cancer


title: GC0642 Gastric Cancer


title: GC0604 Gastric Cancer


title: GC0998 Gastric Cancer


title: GC0627 Gastric Cancer


title: GC1036 Gastric Cancer


title: GC0558 Gastric Cancer


title: GC0570 Gastric Cancer


title: GC0525 Gastric Cancer


title: GC0490 Gastric Cancer


title: GC0480 Gastric Cancer


title: GC0486 Gastric Cancer


title: GC0761 Gastric Cancer


title: GC0442 Gastric Cancer


title: GC0400 Gastric Cancer


title: GC0374 Gastric Cancer


title: GC0295 Gastric Cancer


title: GC0307 Gastric Cancer


title: GC0339 Gastric Cancer


title: GC0382 Gastric Cancer


title: GC0284 Gastric Cancer


title: GC0209 Gastric Cancer


title: GC0422 Gastric Cancer


title: GC0404 Gastric Cancer


title: GC0285 Gastric Cancer


title: GC0182 Gastric Cancer


title: GC0047 Gastric Cancer


title: EC0588 Esophageal Cancer

value: Esophageal Cancer


title: GC0171 Gastric Cancer


title: GC0168 Gastric Cancer


title: EC0581 Esophageal Cancer


title: GC0405 Gastric Cancer


title: GC0417 Gastric Cancer


title: EC0567 Esophageal Cancer


title: EC0562 Esophageal Cancer


title: EC0502 Esophageal Cancer


title: EC0526 Esophageal Cancer


title: EC0515 Esophageal Cancer


title: EC0500 Esophageal Cancer


title: EC0525 Esophageal Cancer


title: EC0499 Esophageal Cancer


title: EC0423 Esophageal Cancer


title: EC0450 Esophageal Cancer


title: EC0483 Esophageal Cancer


title: EC0436 Esophageal Cancer


title: EC0429 Esophageal Cancer


title: GL0071 Glioma


title: GC0742 Gastric Cancer


title: EC0417 Esophageal Cancer


title: GC0573 Gastric Cancer


title: EC0376 Esophageal Cancer


title: EC0385 Esophageal Cancer


title: EC0378 Esophageal Cancer


title: EC0373 Esophageal Cancer


title: EC0351 Esophageal Cancer


title: EC0368 Esophageal Cancer


title: EC0399 Esophageal Cancer


title: EC0302 Esophageal Cancer


title: EC0316 Esophageal Cancer


title: EC0327 Esophageal Cancer


title: EC0426 Esophageal Cancer


title: EC0295 Esophageal Cancer


title: EC0291 Esophageal Cancer


title: EC0457 Esophageal Cancer


title: EC0231 Esophageal Cancer


title: EC0217 Esophageal Cancer


title: EC0363 Esophageal Cancer


title: EC0213 Esophageal Cancer


title: EC0210 Esophageal Cancer


title: EC0209 Esophageal Cancer


title: EC0211 Esophageal Cancer


title: EC0180 Esophageal Cancer


title: EC0162 Esophageal Cancer


title: EC0199 Esophageal Cancer


title: EC0097 Esophageal Cancer


title: EC0095 Esophageal Cancer


title: EC0037 Esophageal Cancer


title: EC0025 Esophageal Cancer


title: EC0045 Esophageal Cancer


title: EC0083 Esophageal Cancer


title: EC0087 Esophageal Cancer


title: EC0064 Esophageal Cancer


title: EC0014 Esophageal Cancer


title: CC1498 Colorectal Cancer

value: Colorectal Cancer


title: CC1497 Colorectal Cancer


title: EC0021 Esophageal Cancer


title: CC1404 Colorectal Cancer


title: CC1522 Colorectal Cancer


title: CC1369 Colorectal Cancer


title: CC1419 Colorectal Cancer


title: CC1485 Colorectal Cancer


title: CC1350 Colorectal Cancer


title: CC1300 Colorectal Cancer


title: CC1262 Colorectal Cancer


title: CC1007 Colorectal Cancer


title: CC1185 Colorectal Cancer


title: CC1112 Colorectal Cancer


title: CC1044 Colorectal Cancer


title: CC1174 Colorectal Cancer


title: CC1188 Colorectal Cancer


title: CC0948 Colorectal Cancer


title: CC1514 Colorectal Cancer


title: CC0896 Colorectal Cancer


title: CC0799 Colorectal Cancer


title: CC0847 Colorectal Cancer


title: CC0844 Colorectal Cancer


title: CC0797 Colorectal Cancer


title: CC0752 Colorectal Cancer


title: CC0672 Colorectal Cancer


title: CC0875 Colorectal Cancer


title: CC0684 Colorectal Cancer


title: CC0710 Colorectal Cancer


title: CC0707 Colorectal Cancer


title: CC0723 Colorectal Cancer


title: CC0564 Colorectal Cancer


title: CC0608 Colorectal Cancer


title: CC0469 Colorectal Cancer


title: CC0801 Colorectal Cancer


title: CC0140 Colorectal Cancer


title: CC0306 Colorectal Cancer


title: CC0368 Colorectal Cancer


title: CC0390 Colorectal Cancer


title: CC0147 Colorectal Cancer


title: CC0225 Colorectal Cancer


title: CC0133 Colorectal Cancer


title: CC0114 Colorectal Cancer


title: CC0784 Colorectal Cancer


title: CC0780 Colorectal Cancer


title: CC0615 Colorectal Cancer


title: CC0092 Colorectal Cancer


title: CC0624 Colorectal Cancer


title: CC0065 Colorectal Cancer


title: BL0513 Bladder Cancer

value: Bladder Cancer


title: BL0509 Bladder Cancer


title: BL0502 Bladder Cancer


title: BL0496 Bladder Cancer


title: CC0135 Colorectal Cancer


title: BL0492 Bladder Cancer


title: BL0488 Bladder Cancer


title: BL0466 Bladder Cancer


title: BL0484 Bladder Cancer


title: BL0461 Bladder Cancer


title: BL0442 Bladder Cancer


title: BL0459 Bladder Cancer


title: BL0449 Bladder Cancer


title: BL0457 Bladder Cancer


title: BL0407 Bladder Cancer


title: BL0433 Bladder Cancer


title: BL0428 Bladder Cancer


title: BL0375 Bladder Cancer


title: BL0348 Bladder Cancer


title: BL0361 Bladder Cancer


title: BL0288 Bladder Cancer


title: BL0315 Bladder Cancer


title: BL0418 Bladder Cancer


title: BL0283 Bladder Cancer


title: BL0437 Bladder Cancer


title: BL0275 Bladder Cancer


title: BL0267 Bladder Cancer


title: CC0922 Colorectal Cancer


title: BL0465 Bladder Cancer


title: BL0199 Bladder Cancer


title: BL0198 Bladder Cancer


title: BL0179 Bladder Cancer


title: BL0155 Bladder Cancer


title: BL0127 Bladder Cancer


title: BL0136 Bladder Cancer


title: BL0134 Bladder Cancer


title: BL0158 Bladder Cancer


title: BL0184 Bladder Cancer


title: BL0114 Bladder Cancer


title: BL0118 Bladder Cancer


title: BL0123 Bladder Cancer


title: BL0051 Bladder Cancer


title: BL0094 Bladder Cancer


title: BL0246 Bladder Cancer


title: BL0056 Bladder Cancer


title: BL0075 Bladder Cancer


title: BL0078 Bladder Cancer


title: BT0401 Biliary Tract Cancer

value: Biliary Tract Cancer


title: BL0046 Bladder Cancer

value: Male


title: BL0206 Bladder Cancer

value: uncertain


title: BT0398 Biliary Tract Cancer


title: BL0030 Bladder Cancer


title: BT0353 Biliary Tract Cancer


title: BL0061 Bladder Cancer


title: BT0372 Biliary Tract Cancer


title: BT0369 Biliary Tract Cancer


title: BT0380 Biliary Tract Cancer


title: BT0396 Biliary Tract Cancer


title: BT0303 Biliary Tract Cancer


title: BT0314 Biliary Tract Cancer


title: BL0013 Bladder Cancer


title: BT0294 Biliary Tract Cancer


title: BT0329 Biliary Tract Cancer


title: BT0390 Biliary Tract Cancer


title: BT0317 Biliary Tract Cancer


title: BT0316 Biliary Tract Cancer


title: BT0307 Biliary Tract Cancer


title: BT0278 Biliary Tract Cancer


title: BT0282 Biliary Tract Cancer


title: BT0292 Biliary Tract Cancer


title: BT0258 Biliary Tract Cancer


title: BT0200 Biliary Tract Cancer


title: BT0257 Biliary Tract Cancer


title: BT0194 Biliary Tract Cancer


title: BT0251 Biliary Tract Cancer


title: BT0232 Biliary Tract Cancer


title: BT0195 Biliary Tract Cancer


title: BT0338 Biliary Tract Cancer


title: BT0163 Biliary Tract Cancer


title: BT0173 Biliary Tract Cancer


title: BT0283 Biliary Tract Cancer


title: BT0179 Biliary Tract Cancer


title: BT0146 Biliary Tract Cancer


title: BT0149 Biliary Tract Cancer


title: BT0203 Biliary Tract Cancer


title: BT0139 Biliary Tract Cancer


title: BT0075 Biliary Tract Cancer


title: BT0211 Biliary Tract Cancer


title: BT0119 Biliary Tract Cancer


title: BT0112 Biliary Tract Cancer


title: BT0043 Biliary Tract Cancer


title: BT0050 Biliary Tract Cancer


title: BT0071 Biliary Tract Cancer


title: BT0127 Biliary Tract Cancer


title: BT0091 Biliary Tract Cancer


title: IMR90 tPBAT Library, HiSeq X Ten

city: Kashiwa

first: Fumihito

last: Miura

state: Chiba

address: Kashiwanoha 5-1-5

department: Graduate School of Frontier Sciences

institute: The University of Tokyo

description:
IMR90_tPBAT
lung, fibroblast-like cell, 16 week embryo

data_processing:
Reads were mapped on mixed reference of human genome hg19 and lambda phage genome using in-house program BMap.
Alignments exported from BMap were summarized into a binary file in graph format using in-house program MPTC.
The methylation levels and coverage were exported from the file in graph format using in-hose program MethExport.
Genome_build: hg19 (GRCh37) and lambda genome
Supplementary_files_format_and_content: bedGraph

source_name: IMR-90 cell

growth_protocol: Cultured in MEM+10%FBS.

extract_protocol:
Genomic DNA was purified using QIAAmp Mini Kit.
Genomic DNA was treated with bisulfite using Methyl Easy Gold Kit from Zymo Research, then adaptor tagging was performed with tPBAT protocol.

treatment_protocol: Cells were removed from culture flask with Trypsin-EDTA and collected by centrifugation.

tag: cell line


title: BT0174 Biliary Tract Cancer


title: BT0212 Biliary Tract Cancer


title: BT0105 Biliary Tract Cancer


title: BT0192 Biliary Tract Cancer


title: WT2-MSC+EC_BM rep2

city: Marseille

first: Stéphane

middle: JC

last: Mancini

address: 27 Boulevard Lei Roure

department: Centre de Recherche en Cancérologie de Marseille

country: France

institute: INSERM

description: normal cells of the bone marrow microenvironment including CD51+ mesenchymal cells and CD31+ enothelial cells

data_processing:
reads alignment, filtering, barcode counting and unique molecular identifier (UMI) counting performed with cellranger version 2.1.1 with Mouse reference dataset-1.2.0
cells/genes matrix generation with cellrangerRkit version 2.0.0
files labeled R1 correspond to the barcode and UMI. The first 16 bases correspond to the barcode and the next 10 correspond to the UMI
files labeled R2 correspond to the biological read and the files labeled I1 correspond to the sample index
Genome_build: mm10 (genome-build GRCm38.p4,genome-version GRCm38,genome-date 2012-01,genome-build-accession NCBI:GCA_000001635.6)
Supplementary_files_format_and_content: csv files (gene/cell matrix)

organism: Mus musculus

source_name: bone marrow mesenchymal and endothelial cells

extract_protocol: 10x Genomics Chromium Single-Cell 3’ v2 protocol

treatment_protocol: CD45-Lin-(B220, CD19, CD11b ,Gr1 ,CD11c ,Ter119, CD117)CD51+CD54+BP1+, CD45-Lin-CD51+CD54-BP1- and CD45-Lin-CD31+ cells from the bone marrow of 8 wo C57Bl/6J mice were sorted by flow cytometry and mixed together

tag: cell type

value: mesenchymal and endothelial cells

tag: tissue

value: Bone marrow

tag: strain

value: 8 weeks old


title: RNA.P14.hep.Ezh1.sexM.2

city: Philadelphia

first: Jessica

middle: Mae

last: Grindheim

state: PA

address: 3400 Civic Center Blvd SCTR 9-169

department: Cell and Developmental Biology

institute: UNIVERSITY OF PENNSYLVANIA

description:
rawCounts.txt
normCounts.txt

data_processing:
Merging: Sequencing replicates were concatenated before alignment.
Alignment: Reads were aligned to NCBI v37/mm9 build from the UCSC Genome Browser with STAR 2.4.2a with the following parameters: ----outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000
Quantitation: Alignments were assigned to mm9 RefSeq (refFlat, from UCSC genome table browser) transcripts with HTSeq v0.6.1p1 and the following arguments: -f sam -r pos -t exon -i gene_id -s no
Differential testing: The count table from HTSeq was normalized and differential gene expression called with DESeq2 v1.14.1
Track creation: Alignments greater than 75bp (corresponding to splicing events) were filtered out to avoid spurious intronic signal.  RPM-normalized bedgraphs were generated with genomeCoverageBed (UCSC utilities), and converted to bigWigs with bedgraphToBigWig (UCSC utilities).
Genome_build: mm9
Supplementary_files_format_and_content: BigWigs represent RPM-normalized RNA signal.  TXT files represent raw (HTseq output) and normalized (DESeq2 output) counts.

source_name: hepatocytes

extract_protocol:
Hepatocytes were resuspended in TRIzol (Thermo Fischer 15596026) and stored at -20°C until the day of library preparation, when RNA was isolated from TRIzol per the manufacturer’s protocol and brought through at least cDNA synthesis all on the same day. RNA isolated from TRIzol was resuspended in TE. Next, total RNA was polyA-selected using 50 μL Invitrogen Dynabeads (dT)25-61002 per the manufacturer’s protocol.  Libraries were prepped from polyA+ RNA using the NEBNext mRNA librarpy prep master mix set for Illumina (NEB E6110) and sequenced with a  NEBNext 500/550 High Output Reagent Cartridge V2 75 cycles (Ref 15057934) and loaded onto the NextSeq 500 for 75bp single-end sequencing.
NEBNext mRNA Library Prep Master Mix Set for Illumina E6110

tag: genotype

value: male

value: postnatal day 14


title: RNA.P14.hep.Ezh1.sexF.1

description:
rawCounts.txt
normCounts.txt

value: female


title: BT0022 Biliary Tract Cancer


title: BT0010 Biliary Tract Cancer


title: RNA.P14.hep.Wt.sexF.2

description:
rawCounts.txt
normCounts.txt

value: Wt


title: BT0100 Biliary Tract Cancer


title: RNA.P14.hep.Wt.sexM.1

description:
rawCounts.txt
normCounts.txt


title: WT rep 4 - cerebellum

city: Chicago

first: Natalie

last: Frederick

address: 303 East Chicago Ave, Ward 10-321

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with read counts per gene

source_name: cerebellum

extract_protocol:
Brain region of interest was isolated using microdissection techniques, flash frozen in liquid nitrogen, and RNA was harvested using Rneasy Plus Universal Mini Kit (Qiagen, cat# 73404).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: cerebellum

value: 6 months

value: wildtype


title: Thap1 cKO rep 3 - striatum

source_name: striatum

value: striatum

value: Thap1 cKO


title: Thap1 cKO rep 2 - striatum


title: Thap1 cKO rep 2 - cerebellum


title: WT rep 1 - cerebellum


title: Thap1 cKO rep 1 - striatum


title: Thap1 cKO rep 3 - cerebellum


title: Thap1 cKO rep 4 - cerebellum


title: Thap1 cKO rep 1 - cerebellum


title: WT rep 3 - striatum


title: WT rep 3 - cerebellum


title: WT-MSC+EC_BM

data_processing:
reads alignment, filtering, barcode counting and unique molecular identifier (UMI) counting performed with cellranger version 2.1.1 with Mouse reference dataset-1.2.0
R1 contains the barcode (first 16 bases) and UMI (next 10 bases).  R2 contains the biological read and I includes the sample index.
cells/genes matrix generation with cellrangerRkit version 2.0.0
Genome_build: mm10 (genome-build GRCm38.p4,genome-version GRCm38,genome-date 2012-01,genome-build-accession NCBI:GCA_000001635.6)
Supplementary_files_format_and_content: csv files (gene/cell matrix)


title: WT rep 2 - striatum


title: WT rep 1 - striatum


title: WT rep 2 - cerebellum


title: M2.hep.Ezh12.sexM.bio3

data_processing:
Merging: Sequencing replicates were concatenated before alignment.
Alignment: Reads were aligned to NCBI v37/mm9 build from the UCSC Genome Browser with STAR 2.4.2a with the following parameters: ----outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000
Quantitation: Alignments were assigned to mm9 RefSeq (refFlat, from UCSC genome table browser) transcripts with HTSeq v0.6.1p1 and the following arguments: -f sam -r pos -t exon -i gene_id -s no
Differential testing: The count table from HTSeq was normalized and differential gene expression called with DESeq2 v1.14.1
Track creation: Alignments greater than 75bp (corresponding to splicing events) were filtered out to avoid spurious intronic signal.  Reads were split into plus and minus strands, RPM-normalized bedgraphs were generated with genomeCoverageBed (UCSC utilities), and converted to bigWigs with bedgraphToBigWig (UCSC utilities).
Genome_build: mm9
Supplementary_files_format_and_content: BigWigs represent plus and minus strand RNA signal.  TXT files represent raw (HTseq output) and normalized (DESeq2 output) counts.

extract_protocol:
Hepatocytes were resuspended in TRIzol (Thermo Fischer 15596026) and stored at -20°C until the day of library preparation, when RNA was isolated from TRIzol per the manufacturer’s protocol and brought through at least cDNA synthesis all on the same day. RNA isolated from TRIzol was resuspended in TE. Next, total RNA was polyA-selected using 50 μL Invitrogen Dynabeads (dT)25-61002 per the manufacturer’s protocol. Sequencing libraries were prepped from polyA+ RNA using the NEBNext Ultra Directional Library Prep Kit for Illumina (NEB 7420), with 12 cycles of PCR using NEBNext Oligos. After library prep, library size was assessed using a Bioanalyzer and Agilent DNA 1000 chip (Agilent 5067-1504), and the concentration of amplifiable DNA assessed with the NEBNext Library Quantification Kit (NEB E7630). Individual libraries were diluted to 2 nM, pooled, and the pooled library requantified with the NEBNext Next Library Quantification Kit. The pooled library was diluted to 3.2 pM using the NEBNext 500/550 High Output Reagent Cartridge V2 75 cycles (Ref 15057934) and loaded onto the NextSeq 500 for 75bp single-end sequencing.
NEBNext Ultra Directional Library Prep Kit for Illumina (NEB 7420)


title: M2.hep.Ezh12.sexF.bio2


title: L-MEP_4_AntiFlag2

city: Houston

first: Daisuke

last: Nakada

state: Texas

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
Library strategy: Cut&Run
Basecalling and fastq generation were performed using Illumina’s software (Casava, bcl2fastq)
Mapping (to mm10) and spike-in normalization were performed using the CutAndRun python scripts available at https://github.com/peteskene
Peaks were called using HOMER (version 4.10)
Motif analysis was performed using HOMER
Genome_build: mm10
Supplementary_files_format_and_content: UCSC formatted bedGraph files, generated using deepTools (bamCoverage); scores are CPM normalized.

source_name: Prdm16s Leukemic-MEP cells

extract_protocol:
200,000 L-MEP were sorted and isolated with antibody for the construction of library using the Cut & Run protocol.
Cut & Run DNA was purified for end repair, adaptor ligation and amplification using KAPA Hyper Prep Kit (Roche, Penzberg, Germany) according to the manufacturer's instructions.

treatment_protocol: We transduced wild-type murine MEP cells with retroviral vectors encoding Prdm16s and transplanted them into syngeneic recipient mice. For library preparation, L-MEPs were sorted from mice that developed leukemia.

tag: chip antibody

value: FLAG antibody (F9291 from Sigma Aldrich, St. Louis, MO)

value: leukemic megakaryocyte-erythroid progenitor (MEP) cells


title: M2.hep.Ezh12.sexM.bio2

tag: Sex


title: L-MEP_3_AntiFlag2


title: M2.hep.Ezh12.sexF.bio1

tag: age


title: M2.hep.Ezh12.sexM.bio1


title: M2.hep.Ezh12.sexF.bio3


title: L-MEP_2_AntiFlag2