title: HCC9_3DPDX_RNA-seq

description:
liver
processed data: PDX_and_PDX3D_RNAseq_rpkm_gene_counts.txt

data_processing:
After checking the read quality by FastQC, raw reads were aligned to hg38 using STAR.
Fragment per kilobase of transcript per million mapped reads (FPKM) was calculated for each gene by HOMER.
Genome_build: hg38
Supplementary_files_format_and_content: PDX_and_PDX3D_RNAseq_rpkm_gene_counts.txt: Tab-delimited text file including transcript FPKM values in PDX and 3DPDX samples.

extract_protocol: RNA quality was assessed by analysis of rRNA band integrity on an Agilent RNA 6000 Nano kit (Agilent Technologies, CA). Ahead of cDNA library construction, the 1ug of total RNA and magnetic beads with Oligo (dT) were used to enrich poly (A) mRNA from it. Then, the purified mRNAs were disrupted into short fragments, and the double-stranded cDNAs were immediately synthesized. The cDNAs was subjected to end-repair, poly (A) addition, and connected with sequencing adapters using the TruSeq RNA sample prep Kit (Illumina, CA). The suitable fragments automatically purified by BluePippin 2% agarose gel cassette (Sage Science, MA) were selected as templates for PCR amplification. The final library sizes and qualities were evaluated electrophoretically with an Agilent High Sensitivity DNA kit (Agilent Technologies, CA) and the fragment was found to be between 350–450 bp. Subsequently, the library was sequenced using an Illumina HiSeq2500 sequencer (Illumina, CA).


title: HCC8_3DPDX_RNA-seq

status: Public on Jan 31 2018

type: SRA

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

country: Canada

institute: Memorial University of Newfoundland

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: Patient-derived HCC

treatment_protocol: No treatment.

tag: tissue origin

value: hepatocellular carcinoma (HCC)

tag: sample type

tag: line


title: HCC12_3DPDX_RNA-seq


title: HCC5_3DPDX_RNA-seq


title: HCC14_3DPDX_RNA-seq


title: HCC6_3DPDX_RNA-seq


title: HCC4_3DPDX_RNA-seq


title: HCC2_3DPDX_RNA-seq


title: HCC3_3DPDX_RNA-seq


title: HCC11_3DPDX_RNA-seq


title: HCC10_3DPDX_RNA-seq


title: HCC7_3DPDX_RNA-seq


title: HCC13_3DPDX_RNA-seq


title: F_6DBF_3

status: Public on Jan 27 2018

city: Beijing

first: Qing

last: Xie

address: No.12 Zhongguancun South St.,Haidian District

country: China

institute: Institute of Vegetables and Flowers,Chinese Academy of Agricultural Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to  Cucumis sativus L. whole genome using TopHat v2.0.12, and mismathch within 2 base is allowed .
Fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM) value of each gene was calculated to estimate gene expression levels (Trapnell et al. 2010).
Genome_build: GCA_000004075.2 ASM407v2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Cucumis sativus

source_name: Ovary

extract_protocol:
Cucumber ovaries and pericarps from numerous-spine and few-spine inbred lines were collected and flash frozen in liquid nitrogen on the same day, with three biological replications of each sample, and RNA were harvested using Trizol reagent.  NEBNext® Ultra™ RNA Library Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: ovary

tag: age

value: 6th  days  before flowering

tag: genotype

value: ns mutant


title: F_6DBF_2


title: HCC3_PDX_RNA-seq

value: HCC-PDX


title: HCC1_PDX_RNA-seq


title: HCC1_3DPDX_RNA-seq


title: HCC10_PDX_RNA-seq


title: HCC5_PDX_RNA-seq


title: HCC4_PDX_RNA-seq


title: HCC13_PDX_RNA-seq


title: HCC9_PDX_RNA-seq


title: HCC6_PDX_RNA-seq


title: HCC12_PDX_RNA-seq


title: HCC7_PDX_RNA-seq


title: HCC11_PDX_RNA-seq


title: HCC8_PDX_RNA-seq


title: HCC2_PDX_RNA-seq


title: HCC14_PDX_RNA-seq


title: F_0DAA_1

source_name: Pericarp

value: pericarp

value: on the day of flowering


title: M_6DBF_3

value: wild type


title: F_0DAA_2


title: M_6DBF_1


title: F_0DAA_3


title: M_0DAA_3


title: M_6DBF_2


title: M_0DAA_2


title: M_0DAA_1


title: H3K4me3_ChIPSeq

status: Public on Jan 25 2018

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Bowtie2
peaks were called using MACS.
Genome_build: hg38
Supplementary_files_format_and_content: Peaks bed files were genetated by MACS

molecule: genomic DNA

source_name: HuH-7 cells

growth_protocol: HuH-7 cells were cultured in DMEM (Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (Gibco), 100 IU/mL penicillin-streptomycin (Gibco) in a 37°C incubator with 5% CO2 and a humidified atmosphere.

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

tag: cell type

value: Liver cancer cells

tag: chip antibody


title: p53_MCF7MT_ChIP1

status: Public on Jan 24 2018

city: Boston

first: Zhi-Min

last: Yuan

state: Massachusetts

address: Goldenson Building, Long wood Ave.

department: School of Public Health

country: USA

institute: Harvard University

data_processing:
Raw fastq files were put through the bcbio-nextgen pipeline for adapter trimming, fastqc quality control, and alignment of reads to the genome (hg19) using Bowtie2.
Peak calling was then done using Macs2 peak caller, searching for narrow peaks which indicate discrete protein binding to genomic DNA.
This was done in two ways: 1) peak calling on all four samples without input control; 2) peak calling on the two mutant samples, using their wildtype counterparts as controls (ie: calling for peaks which are significantly enriched in mutant samples relative to wildtype).
Peaks overlapping between replicates were found using Bedtools. Additionally, to find overlapping as well as reproducible peaks, Macs2 peak calls were ranked according to their p-value, and IDR (irreproducibility discovery rate) analysis was done to find high confidence peaks which were reproduced between the replicates (ie: peaks which show correlation in their rank between replicates).
Peaks were then filtered, choosing only those with IDR rate < 0.05 (ie: highly reproducible).ChIiPQC and ChIPseeker were both run on the set of high confidence, reproducible peaks in R to find the P53 binding profile relative to transcription start site, feature distribution of binding locations. The high confidence peaks were then passed to the DREME online motif discovery tool, which finds significantly enriched motifs in a set of sequences relative to the same set of sequences randomly shuffled as background. Finally, all four alignment files (from initial Bowtie2 alignment) were converted to BigWig format for viewing in IGV – and were scaled and viewed as separate tracks to compare read pileup/peaks in the mutant tracks relative to the wildtype tracks.
Genome_build: Hg19
Supplementary_files_format_and_content: bed.txt files were generated using Macs2 and then applying IDR analysis to replicates. Coordinates indicate regions of enrichment for p53 binding. txt file is a modified bed file from Macs2 for peak calling of mutant vs wildtype samples, and then annotated with gene symbols

growth_protocol: Cells were cultured at 37°C and 5% CO2 in DMEM medium (Corning, Cat.No 10013CV) with 10% fetal bovine serum (Gibco, Cat.No 10082147) and 1% penicillin-streptomycin until about 80% confluent.

extract_protocol:
2X10^6 MCF7 cells were subjected to simpleChIP kit (Cell Signalling Technology, Cat.No, 9003S) following manufacture instructions.
total 25 ng gDNA from each sample was used to construct library with Ultra II DNA library Prep kit (NEB, Cat.No E7645S).

treatment_protocol: No additional treatment applied.

tag: cell line

value: Human breast cancer cell line

tag: er and p53 status

value: ER positive, p53 wild type

tag: genotype/variation

value: MDMX C463A mutation

value: p53 antibody (Santa Cruz, sc-126)


title: p53_MCF7WT_ChIP2


title: F_6DBF_1


title: p53_MCF7WT_ChIP1


title: P493_plus_Tet_3

status: Public on Jan 23 2018

city: Rome

first: Matteo

last: Pallocca

address: Via Fermo Ognibene

country: Italy

institute: Italian National Cancer Institute "Regina Elena"

description: processed data file: fpkm_table_P493_tet.tsv

data_processing:
BaseSpace Illumina Cloud Environment was used for basecalling and demultiplexing.
RNA-seq was analyzed via the web pipeline RAP, which employs the Tuxedo suite for mapping (Tophat) and transcripts reconstruction (Cufflinks, Cuffdiff)
For spikein-normalized data, HTSeq count were normalized using spikein raw counts as scaling factors.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: B-cell lymphoma cell line

extract_protocol:
total RNA was extracted using Qiazol (Invitrogen), purified from genomic DNA contamination through a DNase I (Qiagen) digestion step and further enriched by Qiagen RNeasy columns for gene expression profiling (Qiagen). Quantity and integrity of the extracted RNA were assessed by NanoDrop Spectrophotometer (NanoDrop Technologies) and by Agilent 2100 Bioanalyzer (Agilent Technologies), respectively.
RNA libraries for sequencing were generated in triplicate according to the Illumina TruSeq Stranded Total RNA kit with an initial ribosomal depletion step using Ribo Zero Gold (Illumina, Inc., San Diego, CA, US). Starting material was 500ng of total RNA.

value: B-Cell

tag: treatment

value: 0.1 ug/mL tetracycline for 72h


title: NALM6_CN_1_1

description: processed data file: fpkm_table_nalm-6.tsv

source_name: NALM-6 cell line


title: NALM6_CN_3_1


title: AATF_ChIPSeq_NALM

data_processing:
The data has been analyzed thanks to the CAST pipeline at Cineca, that employs bowtie2 for mapping and MACS2 for peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file

source_name: B-Cell

extract_protocol:
Extract protocol not provided.
Chromatin immunoprecipitations were performed as previously described (Bruno et al, 2002) by using rabbit polyclonal antibodies ChIP grade, anti-Che-1 (Bethyl), and anti c-Myc and Dynabeads Protein G (Life Technologies). The quantity of the immunoprecipitated material was determined by Qubit 2.0 fluorometer (Life Technologies). 10 ng of the immunoprecipitated chromatin was used to prepare the libraries for sequencing following the manufacturer’s instructions including DNA and repairing, adaptor ligation, and amplification (Illumina). The libraries were then sequenced using the Illumina NextSeq 500 system.

value: B-cell

value: anti-Che-1 (Bethyl, A301-032A)


title: P493_plus_Tet_2


title: p53_MCF7MT_ChIP2


title: P493_CN_3

description: processed data file: fpkm_table_P493_siAATF.tsv


title: NALM6_siAATF_2


title: P493_minus_Tet_1


title: NALM6_siMYC_1


title: P493_minus_Tet_3


title: P493_CN_2


title: NALM6_siAATF_3


title: P493_CN_1


title: NALM6_siMYC_3


title: NALM6_siMYC_2


title: P493_siAATF_1


title: P493_minus_Tet_2


title: NALM6_siAATF_1


title: P493_siAATF_3


title: P493_siAATF_2


title: P493_plus_Tet_1


title: NALM6_CN_2_1


title: input DNA NALM

value: none (input)


title: prostate_tumour_CPCG0404

status: Public on Jan 10 2017

type: RNA

city: Toronto

first: Yu-Jia

last: Shiah

state: Ontario

address: MaRS Centre 661 University Avenue Suite 510

department: Informatics and Bio-computing

institute: Ontario Institute for Cancer Research

description:
batch 3
Gene expression data from fresh frozen prostate cancer sample

hyb_protocol: 5.5 ug of single stranded cDNA was hybridized for 16 hr at 45C on Human Gene 2.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix) according to manufacturer’s protocol

data_processing:
All mRNA analysis was performed using R (v3.2.1). Background correction, normalization algorithms and annotation were implemented in the oligo (v1.32.0) package from the BioConductor (v3.0) open-source project. The Robust multichip average (RMA) algorithm was applied to the raw intensity data. Annotations were performed using hugene20sttranscriptcluster.db (v2.13.0) and hta20sttranscriptcluster.db (v8.3.1). The sva package (v3.14.0) was used to correct for batch effects between different arrays.
The file "Normalized_data_with_annotation.txt" contains log2 intensity from RMA and the Entrez Gene ID, Gene symbol, Gene name, and chromosome coordinates.

label: biotin

label_protocol: Biotin end labeled single strand cDNA was prepared according to the Affymetrix GeneChip Whole Transcript (WT) Plus User Manual.

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

value: prostate tumor


title: Rat treated with Pregnant Mare Serum Gonadotropins (PMSG) - Replicate2

status: Public on Jun 30 2017

city: Delhi

first: shah

middle: saddad

last: Hussain

state: Delhi

address: Chhatra marg

department: Zoology

country: India

institute: University of Delhi

description: Replicate 2 of 4.

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to an Agilent Rat Gene Expression Microarray 8x60K (AMADID No: 028279) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327).

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Data extraction from Images was done using Feature Extraction software. Normalization of the data was done in GeneSpring GX : 75th percentile shift method.

organism: Rattus norvegicus

source_name: Ovary, PMSG

label_protocol: The samples for gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double-stranded cDNA. Synthesized double-stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

extract_protocol: Qiagen RNeasy mini kit with DNase treatment following the manufacturer's recommendations.

treatment_protocol: The 26-day-old female rats were injected 50 IU of PMSG (in 0.2 ml of albumin phosphate buffer) and in the control group of animals 0.2 ml of only albumin phosphate buffer injected subcutaneously. After 48 h of the first injection, animals were sacrificed and ovaries were immediately removed and processed.

value: ovary

tag: gender

value: female

value: pregnant mare serum gonadotropin (PMSG)

value: 28 days


title: Rat treated with Pregnant Mare Serum Gonadotropins (PMSG) - Replicate1

description: Replicate 1 of 4.


title: prostate_tumour_CPCG0392


title: Rat treated with Pregnant Mare Serum Gonadotropins (PMSG) - Replicate4

description: Replicate 4 of 4.


title: Rat treated with Pregnant Mare Serum Gonadotropins (PMSG) - Replicate3

description: Replicate 3 of 4.


title: Reference without treatment - Replicate3

description: Replicate 3 of 4.

source_name: Ovary, control

value: vehicle (albumin phosphate buffer)


title: Reference without treatment - Replicate4

description: Replicate 4 of 4.


title: Reference without treatment - Replicate1

description: Replicate 1 of 4.


title: Reference without treatment - Replicate2

description: Replicate 2 of 4.


title: prostate_tumour_CPCG0388


title: prostate_tumour_CPCG0369


title: patient 118 post-transplantation

status: Public on Sep 16 2017

type: genomic

city: Amsterdam

first: Fleur

last: Peters

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC (AMC)

hyb_protocol: Isolated genomic DNA (500 ng) was treated with sodium bisulphite using the EZ-96 DNA methylation kit (Zymo Research, Irvine, CA, USA). Hybridization was performed following manufacturer’s instructions. DNA methylation of CpGs was measured by the Illumina HumanMethylation450K BeadChip using the manufacturer’s protocol (Illumina, Inc., San Diego, CA, USA)

scan_protocol: Array was scanned using the iScan beadchip scanner according to Illumina protocol.

data_processing: All data pre-processing and statistical analysis were performed in R software version 3.2.5. Raw methylation data was normalized with lumi (Bioconductor R) to account for differences between the type I and type II intensities. The data quality was examined using the Methylaid package and all samples passed the five quality controls using the default Methylaid tresholds. Probes with a detection p-value below 0.01 were removed from the dataset. Also probed on sex chromosomes were removed since our patient group was a mixture of male and female.

label: Cy5 and Cy3

source_name: T cells

label_protocol: Standard Infinium Methylation array protocol

extract_protocol: Genomic DNA was extracted using a Qiagen QIAamp Micro kit according to the manufacturers protocol.

treatment_protocol: Flow cytometry assisted cell sorting of the T cells from peripheral blood mononuclear cells.

value: Female

tag: timepoint

value: Post-transplantation

tag: future cscc

value: Yes

tag: current cscc


title: prostate_tumour_CPCG0259


title: MDSC, donor 3 [methylation]

status: Public on Sep 11 2017

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting.

data_processing: preprocesQuantile function from minfi r package.

source_name: CD14 cells treated with IL4/GM-CSF in co-culture with ovarian carcinoma cell line (OVCAR8) for 6 days

label_protocol: Standard Illumina Protocol.

extract_protocol:
Human monocytes were isolated using MACS CD14 microbeads (Milteny) from peripheral blood mononuclear cells using the manufacturer's protocol. After 6 days (in the case of MDSCs, following co-culture), myeloid cells were purified with MACS CD33 microbeads.
Total DNA isolated by standard procedures.

value: myeloid-derived suppressor cells

tag: donor


title: MDSC, donor 2 [methylation]


title: prostate_tumour_CPCG0251


title: prostate_tumour_CPCG0256


title: prostate_tumour_CPCG0208

description:
batch 1
Gene expression data from fresh frozen prostate cancer sample

hyb_protocol: 5.5 ug of single stranded cDNA was hybridized on Human Gene 2.0 ST Arrays.

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

label_protocol: Biotin end labeled single strand cDNA was prepared according to the Affymetrix GeneChip Whole Transcript (WT) terminal labeling and controls Kit


title: prostate_tumour_CPCG0368


title: prostate_tumour_CPCG0184


title: prostate_tumour_CPCG0345


title: prostate_tumour_CPCG0196


title: MDSC, donor 1 [methylation]


title: prostate_tumour_CPCG0191


title: prostate_tumour_CPCG0210


title: prostate_tumour_CPCG0102


title: prostate_tumour_CPCG0099


title: DC, donor 3 [methylation]

source_name: CD14 cells treated with IL4/GM-CSF for 6 days

value: immature dendritic cells


title: patient 116 post-transplantation

value: Male

value: No


title: DC, donor 1 [methylation]


title: DC, donor 2 [methylation]


title: prostate_tumour_CPCG0183


title: prostate_tumour_CPCG0361

description:
batch 2
Gene expression data from fresh frozen prostate cancer sample

hyb_protocol: 5.5 ug of single stranded cDNA was hybridized for 16 hr at 45C on HTA 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.


title: patient 138 post-transplantation


title: patient 143 post-transplantation


title: patient 124 post-transplantation


title: prostate_tumour_CPCG0346


title: patient 129 post-transplantation


title: prostate_tumour_CPCG0334


title: patient 122 post-transplantation


title: patient 103 post-transplantation


title: patient 115 post-transplantation


title: prostate_tumour_CPCG0266


title: patient 134 post-transplantation


title: prostate_tumour_CPCG0364


title: prostate_tumour_CPCG0413


title: prostate_tumour_CPCG0412


title: prostate_tumour_CPCG0411


title: AML12_shCtrl_rep2

status: Public on Dec 03 2017

first: Bo

last: Wen

address: 130 DongAn Road

department: Institutes of Biomedical Sciences

description: Biological replicate 2 of 2. shCtrl AML12 cells.

hyb_protocol: Hybridized to Agilent-027414 arrays.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization. we also smoothed the probe signals using a moving average approach with a window size of 100k bps. The smoothing procedure takes into consideration of the spatial correlation of signals.

organism: Mus musculus

label_protocol: Genomic DNA samples were differentially labeled with Invitrogen’s BioPrime Total for Agilent aCGH labeling kit.

growth_protocol: AML12 cell were kept in complete growth medium：a 1:1 mixture of Dulbecco's modified Eagle's medium and Ham's F12 medium with 0.005 mg/ml insulin, 0.005 mg/ml transferrin, 5 ng/ml selenium, and 40 ng/ml dexamethasone, 90%; fetal bovine serum, 10%.

extract_protocol: 2X1e6 AML12 cells were planted in 6-well plates, and infected with lenti-virus expressing Dam or Dam-Lamin B1 after 48 hours. gDNA was isolated with the Dneasy Tissue kit (Qiagen) per the manufacturers protocol after 72 hours. 2.5 μg of gDNA was digested with DpnI (New England Biolabs), adapters were ligated with T4 ligase (New England Biolabs), and the ligation reaction was subsequently digested with DpnII (New England Biolabs). 500 ng of the DpnII digested material was used as input for a PCR amplification of methylated fragments (MePCR),see Vogel et al., 2008, Nature Protocols for details.

treatment_protocol: The shRNA lentiviruses were prepared as previously described (Fu et al., 2015). Then, 2.5×105 AML12 were infected with the viruses and selected puromycine for 3 days.

value: AML12 cells

tag: condition

value: shCtrl

tag: lenti-virus expression

value: Dam-only


title: prostate_tumour_CPCG0410


title: prostate_tumour_CPCG0362


title: prostate_tumour_CPCG0363


title: AML12_shU_rep2

description: Biological replicate 2 of 2. shU AML12 cells.

value: HNRNPU KD (shU)

value: HNRNPU KD


title: AML12_shU_rep1

description: Biological replicate 1 of 2. shU AML12 cells.


title: prostate_tumour_CPCG0358

value: prostate tumor


title: prostate_tumour_CPCG0409


title: prostate_tumour_CPCG0356


title: prostate_tumour_CPCG0375


title: prostate_tumour_CPCG0378


title: prostate_tumour_CPCG0373


title: prostate_tumour_CPCG0407


title: prostate_tumour_CPCG0381


title: prostate_tumour_CPCG0401


title: prostate_tumour_CPCG0391


title: prostate_tumour_CPCG0357


title: prostate_tumour_CPCG0387


title: prostate_tumour_CPCG0355


title: prostate_tumour_CPCG0354


title: prostate_tumour_CPCG0372


title: prostate_tumour_CPCG0241


title: prostate_tumour_CPCG0366


title: prostate_tumour_CPCG0371


title: prostate_tumour_CPCG0365


title: patient 133 post-transplantation


title: prostate_tumour_CPCG0414


title: prostate_tumour_CPCG0344


title: prostate_tumour_CPCG0341


title: prostate_tumour_CPCG0342


title: prostate_tumour_CPCG0353


title: prostate_tumour_CPCG0352


title: prostate_tumour_CPCG0348


title: prostate_tumour_CPCG0339


title: prostate_tumour_CPCG0340


title: prostate_tumour_CPCG0336


title: prostate_tumour_CPCG0350


title: AML12_shCtrl_rep1

description: Biological replicate 1 of 2. shCtrl AML12 cells.


title: prostate_tumour_CPCG0331


title: prostate_tumour_CPCG0269


title: prostate_tumour_CPCG0324


title: prostate_tumour_CPCG0267


title: prostate_tumour_CPCG0246


title: prostate_tumour_CPCG0236


title: prostate_tumour_CPCG0249


title: prostate_tumour_CPCG0265


title: prostate_tumour_CPCG0263


title: prostate_tumour_CPCG0250


title: prostate_tumour_CPCG0260


title: prostate_tumour_CPCG0258


title: prostate_tumour_CPCG0255


title: prostate_tumour_CPCG0262


title: Human 2, draw 2 - CD4+ T-cells PMA+Ionomycin

status: Public on Dec 29 2016

city: Ithaca

first: Charles

middle: G

last: Danko

state: NY

address: Hungerford Hill Rd

department: Baker Institute

institute: Cornell University

description:
library strategy: PRO-seq
nascent RNA

data_processing:
We trimmed adapter sequences and mapped PRO-seq data using BWA.
Data was converted into bigWig format and converted to reads per kilobase per million mapped (RPKM).
dREG (v. 1.0) was used to identify TREs using the indicated dataset (*TSS.bw).
Genome_build: hg19
Genome_build: panTro4
Genome_build: rheMac3
Genome_build: mm10
Genome_build: rn6
Supplementary_files_format_and_content: Raw dREG scores, peak calls, and PRO-seq or GRO-seq data are provided in standard bigWig or BED file formats.

source_name: Primary Pan-CD4+ cells isolated by positive selection of the CD4 antigen

growth_protocol: CD4+ T-cells isolated from peripheral blood using positive selection for the CD4 antigen.

extract_protocol:
Nuclei were isolated using the protocol in Danko et. al. (2013) Nature Methods.
We prepared PRO-seq libraries as described in Kwak et. al. (2013) Science.

treatment_protocol: Cells were treated for 30 minutes with ethanol+DMSO or PMA+Ionomycin.

value: CD4+ T-cells

tag: species

value: Human

tag: individual

value: PMA+Ionomycin


title: Rhesus Macaque 2 - CD4+ T-cells PMA+Ionomycin

description:
library strategy: PRO-seq
nascent RNA

organism: Macaca mulatta

tag: tissue

value: R. Macaque


title: Human 3 - CD4+ T-cells Untreated

description:
library strategy: PRO-seq
nascent RNA

value: Untreated


title: Chimp 3 - CD4+ T-cells Untreated

description:
library strategy: PRO-seq
nascent RNA

organism: Pan troglodytes

value: Chimp


title: Chimp 5 - CD4+ T-cells Untreated

description:
library strategy: PRO-seq
nascent RNA


title: Chimp 4 - CD4+ T-cells PMA+Ionomycin

description:
library strategy: PRO-seq
nascent RNA


title: Chimp 3 - CD4+ T-cells PMA+Ionomycin

description:
library strategy: PRO-seq
nascent RNA


title: Rhesus Macaque 3 - CD4+ T-cells Untreated

description:
library strategy: PRO-seq
nascent RNA


title: Rhesus Macaque 3 - CD4+ T-cells PMA+Ionomycin

description:
library strategy: PRO-seq
nascent RNA


title: Mouse Untreated

description:
library strategy: PRO-seq
nascent RNA

value: Mouse


title: prostate_tumour_CPCG0248


title: Rhesus Macaque 1 - CD4+ T-cells Untreated

description:
library strategy: PRO-seq
nascent RNA


title: Human 1 - CD4+ T-cells Untreated

description:
library strategy: PRO-seq
nascent RNA


title: Human 2, draw 1 - CD4+ T-cells PMA+Ionomycin

description:
library strategy: PRO-seq
nascent RNA


title: Human 2, draw 2 - CD4+ T-cells Untreated

description:
library strategy: PRO-seq
nascent RNA


title: Human 3 - CD4+ T-cells PMA+Ionomycin

description:
library strategy: PRO-seq
nascent RNA


title: Chimp 4 - CD4+ T-cells Untreated

description:
library strategy: PRO-seq
nascent RNA


title: Rhesus Macaque 2 - CD4+ T-cells Untreated

description:
library strategy: PRO-seq
nascent RNA


title: Rat Untreated

description:
library strategy: PRO-seq
nascent RNA

value: Rat


title: Chimp 5 - CD4+ T-cells PMA+Ionomycin

description:
library strategy: PRO-seq
nascent RNA


title: Human 1 - CD4+ T-cells PMA+Ionomycin

description:
library strategy: PRO-seq
nascent RNA


title: D53B90

status: Public on Nov 02 2016

city: Groningen

first: Jan Maarten

last: van Dijl

address: Hanzeplein 1

institute: University Medical Groningen

data_processing:
Bacterial ribosomal RNA was depleted
cDNA library was prepared according to the manufacturer’s protocol (Illumina, US)
cDNA sequencing of samples was performed with paired-end reads (PE100) with HiSeq2000 sequencing lane (Otogenetics, USA)
Processing of the data was done against USA300_FPR3757.

organism: Staphylococcus aureus subsp. aureus USA300

source_name: Clinical isolate from infected human

growth_protocol: Bacterial isolates were grown in duplicate overnight (14-16 h) in 25 mL Tryptic Soy Broth (TSB; Oxoid) under vigorous shaking (115 rpm) at 37°C in a water bath. The cultures were then diluted into 25 mL pre-warmed RPMI 1640 medium supplemented with 2 mM glutamine (GE Healthcare/PAA, Little Chalfont, United Kingdom) to an OD600 of 0.05 and cultivation was continued under the same conditions. Exponentially growing cells with an OD600 of ~0.5 were re-diluted into 120 mL fresh, pre-warmed RPMI medium to a final OD600 of 0.05. The cultivation was continued till 90 min into the stationary growth phase, where the cultures had an OD600 of ~1.3.  15 ml of culture aliquots were collected for RNA isolation at mid exponential and 90 min into the stationar growth phases.

extract_protocol:
Total RNA was isolated by phenol-chloroform extraction as described previously. Samples were processed twice with an equal volume of acid phenol solution (Sigma-Aldrich, Zwijndrecht, The Netherlands), and mixed thoroughly on an Eppendorf tube shaker until completely thawed. The resulting suspension was then centrifuged for 5 min, 12000 rpm, and the supernatant was transferred into a fresh microcentrifuge tube. Next, samples were processed once with one volume of Chloroform/isoamyl alcohol, mixed well, and centrifuged for 5 min, 12000 rpm. RNA was precipitated from the supernatant by the addition of 1/10 volume of 3 M Na-Acetate, pH 5.2, and 0.8 ml of isopropanol. The precipitated RNA was washed once with 80 % RNase-free Ethanol, and dissolved in RNase-free water. Lastly, residual DNA was removed by treating the RNA sample with the RNase-Free DNase the Set kit (Qiagen) and the RNA was purified using the RNA Clean-Up and Concentration Micro Kit (Norgen
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: isolate

value: hospital assocated

tag: growth phase

value: stationary


title: D61B90

value: community associated


title: D69A90


title: D53A90


title: D66B90


title: D66A90


title: D69B90


title: D30B90

data_processing:
Bacterial ribosomal RNA was depleted
cDNA library was prepared according to the manufacturer’s protocol (Illumina, US)
cDNA sequencing of samples was performed with paired-end reads (PE100) with HiSeq2000 sequencing lane (Otogenetics, USA)
Processing of the data was done against USA300_FPR3757.
Processing of the data was done against USA300_FPR3757.


title: D15B90


title: D17A90


title: D29B90


title: D22A90


title: D32B90


title: D30A90


title: D37A90


title: D3B90


title: D22B90


title: D15A90


title: D17B90


title: D3A90


title: D61A90


title: D32A90


title: D37B90


title: D69A0.5

value: exponential


title: D66A0.5


title: D61B0.5


title: D29A90


title: D61A0.5


title: D53A0.5


title: D53B0.5


title: D69B0.5


title: D32A0.5


title: D37A0.5


title: D32B0.5


title: D30B0.5


title: D30A0.5


title: D66B0.5


title: D29B0.5


title: D22A0.5


title: D22B0.5


title: D17A0.5


title: D29A0.5


title: D15B0.5


title: D15A0.5


title: D3B0.5


title: D3A0.5


title: D37B0.5


title: D17B0.5


title: Diagnostic_DLBCL_sample_H371 [re-analysis]

status: Public on Oct 05 2016

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

country: Denmark

institute: Aalborg University Hospital

hyb_protocol: Included in the label protocol.

scan_protocol: Gene Chips were scanned using the Affymetrix GeneChip scanner 3000 7G

data_processing:
Data were analyzed using R version 3.0.2 and several R and Bioconductor packages and Partek Genomics Suite version 6.6. The .CEL files were pre-processed in Partek using the Robust Multichip Average procedure (RMA) and scan date and labelling kit were set as random effects.
The .CEL files were pre-processed in Partek Genomics Suite version 6.6. RMA normalization was used and scan date and labelling kit were set as random effects.

source_name: diagnostic diffuse large B-cell lymphoma sample

label_protocol: Biotinylated cRNA were prepared using the GeneChip 3' IVT Express Kit (#P/N901229, Affymetrix) from 100 ng total RNA using manual P/N702646 Rev.4.

extract_protocol: Total RNA was purified from frozen diagnostic DLBCLs by homogenizing the sample in Trizol and incubating for 5 minutes at RT. 200µl chloroform was added and incubated 2 minutes at RT, the mixture was centrifuged at 12,000 g for 10 minutes at 4°C. The aqueous phase was transferred to a new tube and 100 % ethanol added in 1.25X the volume. Mix well and transfer to mirVANA columns (#1561, Ambion) and follow the manufacturer’s instruction from this point.

treatment_protocol: Diagnostic samples of diffuse large B-cell lymphoma (DLBCL)

value: diagnostic diffuse large B-cell lymphoma (DLBCL)

tag: abc/gcb class

value: ABC

tag: bags class

value: Centrocyte

tag: the regs probability of resistance towards doxorubicin (h)

tag: ipi status

value: Diagnosis through autopsy


title: Diagnostic_DLBCL_sample_H439 [re-analysis]

value: GCB

tag: treatment

value: R-CHOP


title: Diagnostic_DLBCL_sample_H450 [re-analysis]

value: Memory


title: Diagnostic_DLBCL_sample_H344 [re-analysis]


title: Diagnostic_DLBCL_sample_H484 [re-analysis]

value: Plasmablast


title: Diagnostic_DLBCL_sample_H297 [re-analysis]

value: R-CHOEP


title: Diagnostic_DLBCL_sample_H284 [re-analysis]


title: Diagnostic_DLBCL_sample_H479 [re-analysis]

value: Centroblast


title: Diagnostic_DLBCL_sample_H333 [re-analysis]


title: Diagnostic_DLBCL_sample_H345 [re-analysis]


title: Diagnostic_DLBCL_sample_H300 [re-analysis]


title: H576

description:
Gene expression data at time of DLBCL diagnosis
H576_(HG-U133_Plus_2).CEL

hyb_protocol: Userguide GeneChip 3' IVT PLUS Reagent Kit P/N 703210 Rev. 2

data_processing: Data were analyzed using R version 3.0.2 and several R and Bioconductor packages and Partek Genomics Suite version 6.6. The .CEL files were pre-processed in Partek using the Robust Multichip Average procedure (RMA) together with the samples of GSE56315 referred to in the field overall design and scan date and labelling kit were set as random effects.

label: Biotin

source_name: DLBCL patient_lymph node

label_protocol: 3' IVT PLUS Reagent Kit Affymetrix P/N 703210 Rev. 2

extract_protocol: Total RNA was extracted using the Invitrogen TRIzol Reagent combined with the mirVana miRNA Isolation kit. RNA quality was checked using an Agilent 2100 Bioanalyzer and the concentration measured with Nanodrop ND-1000 spectrophotometer. cDNA generated using the Ambion WT Expression Kit (PN 4411984), following manufacturer's instructions.

treatment_protocol: The tumor sample was after removal snap frozen and stored in OCT at -80ºC. From each OCT block, a small fraction of the sample was removed using a scalpel, washed twice in PBS, and homogenized using the TissueLyser II (Qiagen).

tag: subject status

value: Diffuse large B-cell lymphoma (DLBCL) patient

value: lymph node

tag: probability of being sensitive to doxorubicin

value: Fludarabin


title: H544

description:
Gene expression data at time of DLBCL diagnosis
H544_(HG-U133_Plus_2).CEL


title: Mouse-C3H cbe3

status: Public on Aug 30 2016

city: Rehovot

first: Tony

last: Futerman

address: Herzl 234

country: Israel

institute: Weizmann institute of science

hyb_protocol: 3ug ss cDNA in 130 ul were hybridized to a Mouse Gene 2.0 ST array and hybridized for 17 hours at 45° at 60rpm using GeneChip Hybridization, Wash and Stain Kit materials (Affymetrix, #900720). Post-hyb washes were done with Affymetrix wash solutions on the FS450 station using FS450_0002 protocol.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 3000 7G

data_processing: The data was analyzed with Partek Genomic Suite version 6.6 , (Partek Inc., St. Louis, Missouri 63141, http://www.partek.com), using RMA.

source_name: C3H cbe

label_protocol: Synthesis of cDNA was performed using the GeneChip WT PLUS Reagent Kit (Affymetrix, #902280). A starting amount of 100 ng total RNA was used for each sample. Purified cRNA was enzymatically fragmented and biotinylated using GeneChip WT Terminal Labeling Kit (Affymetrix, #900670).

growth_protocol: CBE-treated mice were used as a model of nGD and PBS-treated as healthy controls. Mice were treated from day 8-18, sacrificed and their brains removed and placed on a Young Mouse Brain Slicer Matrix (BSMYS001-1, Zivic instruments, PA, USA). Single-edge razor blades were inserted into the matrix to generate 1 mm coronal sections. The section containing the cortex was snap-frozen on dry ice.The sample was placed in an Eppendorf tube, snap-frozen in liquid N2 and stored at -80°C. All dissection tools were first cleaned with surface decontaminate RNase away (Molecular BioProducts, Inc., San Diego, CA).

extract_protocol: Total RNA was isolated using the RNeasy mini kit (Qiagen) according to manufacturer’s instructions, which included a DNase step and addition of β-mercaptoethanol.

tag: age

value: 18 days old

tag: Sex

value: male

tag: agent

value: CBE

tag: disease state

value: model of nGD

value: cortex, brain tissue


title: H563

description:
Gene expression data at time of DLBCL diagnosis
H563_(HG-U133_Plus_2).CEL


title: H553

description:
Gene expression data at time of DLBCL diagnosis
H553_(HG-U133_Plus_2).CEL


title: Mouse-C3H pbs3

source_name: C3H pbs

value: PBS

value: healthy control


title: Mouse-C3H cbe1


title: Diagnostic_DLBCL_sample_H285 [re-analysis]

value: diagnostic diffuse large B-cell lymphoma (DLBCL)


title: H572

description:
Gene expression data at time of DLBCL diagnosis
H572_(HG-U133_Plus_2).CEL

value: ABC


title: H578

description:
Gene expression data at time of DLBCL diagnosis
H578_(HG-U133_Plus_2).CEL

value: GCB

value: Naive

value: Rituximab


title: H574

description:
Gene expression data at time of DLBCL diagnosis
H574_(HG-U133_Plus_2).CEL

value: Centrocyte

value: CHOP


title: H552

description:
Gene expression data at time of DLBCL diagnosis
H552_(HG-U133_Plus_2).CEL

value: Diffuse large B-cell lymphoma (DLBCL) patient

value: R-CHOP


title: Mouse-C3H pbs2


title: H545

description:
Gene expression data at time of DLBCL diagnosis
H545_(HG-U133_Plus_2).CEL

value: lymph node

value: R-CEOP


title: H551

description:
Gene expression data at time of DLBCL diagnosis
H551_(HG-U133_Plus_2).CEL

value: R-CVP


title: Mouse-C3H cbe2

value: 18 days old

value: male

value: CBE


title: H558

description:
Gene expression data at time of DLBCL diagnosis
H558_(HG-U133_Plus_2).CEL

value: Plasmablast


title: Mouse-C3H pbs1

value: PBS

value: healthy control

value: cortex, brain tissue


title: Mouse-C57 cbe3

source_name: C57 cbe

value: model of nGD


title: H564

description:
Gene expression data at time of DLBCL diagnosis
H564_(HG-U133_Plus_2).CEL

value: ABC


title: Mouse-C57 cbe2


title: Mouse-C57 pbs1

source_name: C57 pbs


title: Mouse-FVB cbe1

source_name: FVB cbe

value: FVB


title: Mouse-FVB cbe3


title: Mouse-C57 cbe1


title: Mouse-FVB pbs2

source_name: FVB pbs


title: Mouse-C57 pbs2


title: Mouse-C57 pbs3


title: Mouse-FVB pbs3


title: Mouse-FVB pbs1


title: Mouse-FVB cbe2


title: Mouse-SV129 pbs3

source_name: SV129 pbs


title: MF.PC.SPF#3

status: Public on Nov 20 2015

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

source_name: Peritoneal Cavity

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

value: 6 Weeks Old

tag: genetic background

value: Male

tag: cell family

value: Macrophage

tag: phenotype markers

tag: separation method

value: Dissection / Trimming

tag: amplification technique

value: Ambion WT Expression Kit


title: Mouse-SV129 pbs2

tag: strain

tag: tissue


title: Mouse-SV129 cbe1

source_name: SV129 cbe


title: MF.PC.SPF#2

tag: source prep description

value: Spleen dissocation and stain


title: Mouse-SV129 cbe3


title: Patient sample FL200

status: Public on Jul 16 2015

first: Robert

last: Kridel

state: ON

address: 101 College Street, Rm 12-311

institute: Princess Margaret Cancer Centre

hyb_protocol: labeled PCR products were hybridized to HT-12v4 BeadChips and washed following Illumina's standard protocols

scan_protocol: beadchips were scanned using the Illumina BeadArray System

data_processing: Normalization was performed using the quantile normalization setting in the normaliseIllumina function from the beadarray R package.

source_name: Follicular lymphoma

label_protocol: 400ng of FFPET total RNA was converted to cDNA, followed by an amplification step using the Illumina Human Whole-Genome DASL HT Assay kit (catalogue #DA-905-0096, San Diego, CA, US)

growth_protocol: primary patient samples, formalin-fixed and paraffin-embedded

extract_protocol: Roche High Pure RNA Paraffin kit

value: Follicular lymphoma

tag: codeffs

tag: ffs

tag: codeos

tag: os

value: not determined

tag: ecog

tag: crebbp

tag: m7-flipi score


title: Mouse-SV129 pbs1

tag: age

value: 18 days old

tag: Sex

value: male

tag: agent


title: Patient sample FL197

value: Female


title: Patient sample FL192


title: Patient sample FL196


title: Patient sample FL190


title: Patient sample FL195


title: MF.PC.SPF#1

tag: genetic background

tag: cell family


title: Patient sample FL199


title: Patient sample FL198


title: Patient sample FL176


title: Patient sample FL181


title: Patient sample FL191


title: Patient sample FL187


title: Patient sample FL193


title: Patient sample FL194


title: Patient sample FL185


title: Patient sample FL184


title: Patient sample FL170


title: Patient sample FL167


title: Patient sample FL168


title: Patient sample FL169


title: Patient sample FL173


title: Patient sample FL153


title: Patient sample FL158


title: Mouse-SV129 cbe2

value: CBE

tag: disease state


title: Patient sample FL147


title: Patient sample FL140


title: Patient sample FL152


title: Patient sample FL151


title: Patient sample FL141


title: Patient sample FL148


title: Patient sample FL145


title: Patient sample FL139


title: Patient sample FL154


title: Patient sample FL156


title: Patient sample FL150


title: Patient sample FL159


title: Patient sample FL137


title: Patient sample FL138


title: Patient sample FL149


title: Patient sample FL144


title: Patient sample FL136


title: Patient sample FL130


title: Patient sample FL133


title: Patient sample FL135


title: Patient sample FL134


title: Patient sample FL132


title: Patient sample FL126


title: Patient sample FL127


title: Patient sample FL121


title: Patient sample FL123


title: Patient sample FL115


title: Patient sample FL146


title: Patient sample FL120


title: Patient sample FL114


title: Patient sample FL116


title: Patient sample FL122


title: Patient sample FL112


title: Patient sample FL129


title: Patient sample FL119


title: Patient sample FL101


title: Patient sample FL106


title: Patient sample FL103


title: Patient sample FL110


title: Patient sample FL099


title: Patient sample FL097


title: Patient sample FL111


title: Patient sample FL102


title: Patient sample FL094


title: Patient sample FL107


title: Patient sample FL118


title: Patient sample FL096


title: Patient sample FL095


title: Patient sample FL092


title: Patient sample FL098


title: Patient sample FL077


title: Patient sample FL087


title: Patient sample FL088


title: Patient sample FL086


title: Patient sample FL073


title: Patient sample FL078


title: Patient sample FL089


title: Patient sample FL090


title: Patient sample FL069


title: Patient sample FL066


title: Patient sample FL076


title: Patient sample FL071


title: Patient sample FL100


title: Patient sample FL083


title: Patient sample FL075


title: Patient sample FL082


title: Patient sample FL068


title: Patient sample FL065


title: Patient sample FL067


title: Patient sample FL063


title: Patient sample FL060


title: Patient sample FL064


title: Patient sample FL061


title: Patient sample FL056


title: Patient sample FL059


title: Patient sample FL057


title: Patient sample FL062


title: Patient sample FL053


title: Patient sample FL047


title: Patient sample FL051


title: Patient sample FL049


title: Patient sample FL052


title: Patient sample FL050


title: Patient sample FL038


title: Patient sample FL034


title: Patient sample FL045


title: Patient sample FL040


title: Patient sample FL030


title: Patient sample FL027


title: Patient sample FL035


title: Patient sample FL032


title: Patient sample FL046


title: Patient sample FL021


title: Patient sample FL041


title: Patient sample FL017


title: Patient sample FL028


title: Patient sample FL033


title: Patient sample FL029


title: Patient sample FL019


title: Patient sample FL022


title: Patient sample FL043


title: Patient sample FL036


title: Patient sample FL024


title: Patient sample FL039


title: Patient sample FL042


title: Patient sample FL117


title: MF.PC.2h.IFN#1

tag: phenotype markers

tag: separation method

tag: amplification technique


title: Patient sample FL009

tag: tissue


title: Patient sample FL010

tag: codeffs


title: Patient sample FL007

tag: ffs


title: Patient sample FL006

tag: codeos


title: Patient sample FL008

tag: os


title: Patient sample FL080

tag: ecog


title: Patient sample FL001

tag: crebbp


title: Patient sample FL004

tag: m7-flipi score


title: Genome-engineered organoid6

status: Public on Jan 18 2015

city: Tokyo

first: Mariko

last: Shimokawa

address: 35, Shinanomachi, Shinjuku-Ku

country: Japan

institute: Keio University

description: genome engineered organoids

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip PrimeView Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with GeneSpring GX 12 using RMA as summarization algorithm and  baseline to median of all samples.

source_name: genome-engineered organoids from human colon organoids

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (3'IVT Express Kit User Manual,Affymetrix).

growth_protocol: Dissociated single cells derived from indicated organoids were cultured for 7 days.

extract_protocol: Extraction of total RNA with Rneasy Plus Mini Kit (QIAGEN) was performed according to the manufacturer's instructions.

treatment_protocol: Not applicable

tag: genetic modification

value: BKSTP (Lenti virus vector)


title: Modifed Adenoma3

source_name: colon epithelial organoid

value: Adenoma

value: KRAS G12V knock in


title: CRC9

source_name: metastasized colorectal cancer organoid

tag: source tissue

value: metastasized colorectal cancer (LM CRC)

value: LM CRC

value: metastasized colorectal cancer organoid


title: CRC8


title: Adenoma1

source_name: colon adenoma organoid

value: benign adenoma

value: colon adenoma organoid


title: Patient Derived Xenograft LTL-313H-G7

status: Public on Jan 12 2013

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

institute: Vancouver Prostate Centre

hyb_protocol: 600ng labeled cRNA was hybridized on Agilent SurePrint G3 Human GE 8x60K Microarray (Design ID 028004)

scan_protocol: Slides were scanned with the Agilent DNA Microarray Scanner at a 3um scan resolution using the one colour and 20 bit tiff file settings

data_processing: Image files were processed with Agilent Feature Extraction 10.10 to produce spatially detrended and background subtracted gProcessedSignal intensities, and quantile-normalized using Genespring.

source_name: Prostate Tumor

label_protocol: 100ng of total RNA was used as input for generation of Cyanine-3-labeled cRNA following Agilent’s One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.0.

extract_protocol: Trizol

value: prostate cancer tumor

tag: patient source

tag: tumor foci

value: Patient Derived Xenograft


title: Adenoma2


title: Adenoma4


title: Genome-engineered organoid2

description: genome engineered organoids

value: AKST (CRISPR/Cas9)

value: genome-engineered organoids from human colon organoids


title: Patient Derived Xenograft LTL-331R


title: Patient Derived Xenograft LTL-418-G6


title: Modifed Adenoma1

value: Smad4 deletion


title: Patient Derived Xenograft LTL-412-G5


title: CRC6

source_name: colorectal cancer organoid

value: primary colorectal cancer (CRC)

value: primary CRC

value: colorectal cancer organoid


title: CRC5


title: CRC1


title: Genome-engineered organoid4

description: genome engineered organoids


title: Genome-engineered organoid1

description: genome engineered organoids

value: A (CRISPR/Cas9)


title: CRC3


title: CRC4


title: Genome-engineered organoid5

description: genome engineered organoids

value: BKST (Lenti virus vector)


title: Adenoma5


title: Adenoma3


title: CRC2


title: Patient Derived Xenograft LTL-352-G13


title: Genome-engineered organoid3

description: genome engineered organoids

value: AKSTP (CRISPR/Cas9)


title: CRC7


title: Patient Derived Xenograft LTL-313H-G16


title: Patient sample FL002

value: Follicular lymphoma

tag: age

tag: Sex

value: Male


title: Patient Derived Xenograft LTL-313D


title: Patient Derived Xenograft LTL-313C


title: Patient Derived Xenograft LTL-313BR


title: Patient Derived Xenograft LTL-313A


title: Patient Derived Xenograft LTL-313B-G5


title: Patient Derived Xenograft LTL-313B-G8


title: HuH7 cells, replicate 1

status: Public on Oct 01 2012

city: Singapore

first: jinmiao

last: chen

address: Biopolis

country: Singapore

institute: Singapore Immunology Network

description: human hepatoma cell line

hyb_protocol: Target samples were hybridized to Human Exon 1.0 ST microarrays according to the manufacturer's protocols in a Affymetrix hybridization oven

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was RMA normalized and gene level intensity determined with Affymetrix Power tools. The 95th percentile of the negative control (128) was taken as the cutoff for expression.  Genes expressed in all 4 cell lines on chromosome 6 were considered for further analysis.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: cell line

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: 37°C, 5% CO2, humidified incubator. Culture medium: RPMI1640, 10% Fetal BovineSerum, L-Gln 2 mM, Na-pyruvate 1 mM, non-essential aminoacids 1 mM, Kanamycin 100 µg/ml.

extract_protocol: Total RNA was extracted following the double extraction protocol:  RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (Trizol Invitrogen) followed by a Qiagen RNeasy clean-up procedure.

tag: cell line

tag: cell type

value: hepatoma


title: Patient Derived Xenograft LTL-311-G8


title: BS125-3 cells, replicate 3

description: human glioblastoma cell line

value: glioblastoma


title: THP-1 cells, replicate 3

description: human AML cell line

value: acute monocytic leukemia


title: THP-1 cells, replicate 1

description: human AML cell line


title: HuH7 cells, replicate 2

description: human hepatoma cell line


title: BS125-3 cells, replicate 1

description: human glioblastoma cell line


title: THP-1 cells, replicate 2

description: human AML cell line


title: HuH7 cells, replicate 3

description: human hepatoma cell line


title: BS125-3 cells, replicate 2

description: human glioblastoma cell line


title: A375 cells, replictate 2

description: human melanoma cell line

value: melanoma


title: A375 cells, replicate 1

description: human melanoma cell line


title: A375 cells, replicate 3

description: human melanoma cell line


title: Patient Derived Xenograft LTL-313H

data_processing:
Image files were processed with Agilent Feature Extraction 10.10 to produce spatially detrended and background subtracted gProcessedSignal intensities
Please see accompanying excel file: Xenograft_Expression_Normalized_Genespring-Export_Sept2012_forGEO.txt which includes the Genepring output of quantile normalized values for each of the above samples.

value: prostate cancer tumor


title: Clinical Patient-1015

tag: individual

value: patient 1015

value: Clinical Patient


title: Patient Derived Xenograft LTL-313B

tag: tissue

value: Patient Derived Xenograft


title: Patient Derived Xenograft LTL-370


title: Patient Derived Xenograft LTL-310


title: Clinical Patient-1005

value: patient 1005


title: Patient Derived Xenograft LTL-412

value: Patient 1005


title: Patient Derived Xenograft LTL-418

value: Patient 1015


title: Patient Derived Xenograft LTL-331

value: Patient 927


title: Clinical Patient-927

value: patient 927


title: Patient Derived Xenograft LTL-311


title: Recurrent Adenocarcinoma 7

status: Public on Jun 04 2007

city: Hannover

first: Astrid

last: Rohrbeck

state: Niedersachsen

address: Carl-Neuberg-Straße 1

department: Department of Toxicology

country: Germany

institute: Medizinische Hochschule Hannover

description: Laser capture lung cancer cells

hyb_protocol: Arrays were prehybridizised for 10 minutes using 140µl MES- hybridization buffer (70,4g MES free acid monohydrate, 193.3g MES Sodium Salt, 800ml accugen water, pH 6.5 – 6.7) and 140µl aqua dest. at 45°C and 60rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix). After removal of the pre-hybridizing solution, the array is loaded with 250 µl of the hybridizing solution (30µl fragmented aRNA, 5µl control-oligo B2, 15µl 20x Eukaryotic hybridizing control, 3µl salmon sperm-DNA, 3µl azetylic BSA, 150µl 2x MES- Hybridizing buffer and 94µl aqua dest.). Following 16-hour incubation at 45°C with permanent rotation, the hybridizing solution is removed. The array is loaded with 280µl of washing buffer A (300ml 20x SSPE, 1ml 10% Tween 20, 698ml accugen water) and a maximum of 4 hybridized arrays are put into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B (83.3ml 12x MES, 5.2ml 5M NaCl, 1ml 10% Tween 20, 910.5ml accugen water) using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus Oligonukleotid- Arrays = Midi-euk2v3). During washing procedure the staining solution is prepared: Staining solution: 600µl 2x Staining Buffer 540µl dH2O 48µl BSA 12µl Streptavidine- Phycoerythrin- Conjugate Array is incubated with 600µl of the staining solution after washing for 40 minutes followed by incubation with the antibody solution for 10 minutes: Antibody solution: 300µl 2x Staining Buffer 266 4µl dH2O 24µl BSA 6µl Goat IgG 3.6µl biotinylated Anti- Streptavidin- AB After removal of the antibody solution 600µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.

scan_protocol: (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome phycoerythrin at a wave length of 488nm with an emission at 570nm.

data_processing: Using the affy package of functions of statistical scripting language 'R' integrated into the Bioconductor project data from cel files of each sample were normalized by variance stabilizing transformations (VSN) Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics 2002;18:96-104.

label: Biotin/Streptavidin-PE

source_name: recurrent AC (stage IIIB or IV)

label_protocol:
Amplification, reverse transcription and labelling of the sample.
For amplification of micro-dissected RNA, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used.
Between 200-500ng of isolated RNA were transcribed into cDNA.
First strand cDNA- Synthesis:
11µl (RNA or RNA and dH2O) Sample
1µl Oligo(dT)Primer
70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
Reaction kit:
2µl 10x First Strand Buffer
1µl Ribonuclease Inhibitor
4µl dNTP Mix
Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
Second strand cDNA- Synthese:
63µl Nuclease-free Water
10µl 10x Second Strand Buffer
4µl dNTP Mix
1µl RNase H
For second strand sythesis 2µl der DNA- Polymerase are added followed by a 2 h incubation at 42°C.
Purification of cDNA:
Final elution volume = 16 µl and storage for 12 h at -20°C
Labelling with in vitro transcription using biotin labelled nucleotides:
Labeling mix:
4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit, Enzo Life Sciences, Farmingdale)
4µl T7 10x reaction buffer
12µl RNase free water
The labelling mix is incubated with the sample and 4µl of the enzyme mix is added followed by an incubation period of 5 hours at 37°C. The amplified RNA is
purified and is eluted in a final volume of 96 µl.
Quality control of aRNA:
The concentration and purity of aRNA is measured using the NanoDrop ND-1000 (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
The OD 260/OD 280 aRNA was between 1.7 and 2. To exclude the possibility of degradation and/or contamination RNA was analyzed again using a Agilent 2100
Bioanalyzer (Agilent Technologies, Palo Alto CA).
Fragmentation:
For optimal hybridization with the complementary oligonucleodid sequences, a fragmentation of the amplified RNA was performed.
24µl of the sample were added to 6µl of fragmentation buffer (200mM TRIS-Acetat, ph 8.2, 500mM KOAc, 150mM MgOAc, Affymetrix) and incubated at 94°C for 35
minutes.

extract_protocol:
RNA of LCM-tumor cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the
kit and were applied according to the manufacturer’s instructions.
In brief:
LCM tumor cells suspended in 350µl lysis buffer were incubated with 350µl 70% ethanol.
700µl suspension was put on RNeasy MinElute- column and spun down for one minute with 10,000 rpm.
DNase- digestion (10µl DNase+70µl RDD buffer-> 80µl) for 15 at 30°C.
2 washing steps with 350µl RW1- buffer and 500µl RPE- buffer.
500µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2 minutes with 10,000 rpm.
Removal of ethanol: column was spun down for 5 minutes with 30,000 rpm.
Elution of RNA with 14µl of RNAse free water.
Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
GmbH, Erlangen). Purified RNA was stored at -80°C.

tag: gender

value: m

tag: disease

value: recurrent AC

tag: received platinum-based therapy with progression

value: yes


title: PHA stimulated, Tempus, replicate U (Blood_PHA25_ABI_U)

status: Public on Oct 30 2008

city: Baltimore

first: Zhong

last: Gao

state: MD

address: Ross 844 720 Rutland Avenue

institute: Johns Hopkins University

description: PHA stimulated, Tempus RNA extraction method, replicate U

hyb_protocol: Hybridization on Affymetrix HG-U133 2.0 plus array according to manufacturer's instructions.

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

data_processing: The data normalizaion was performed using Bioconductor package THREESTEP(background.method="MASIM", noemalize.method="scaling", summary.method="tukey.biweight").

source_name: Peripheral blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol. cRNA target amplificationwas performed using the Affymetrix In-vitro Transcription (IVT) Kit followed by a Globin Reduction step.

extract_protocol: RNA was extracted at the ITN Central Nucleic Acid Isolation Core facility, Pittsburgh, PA according to the ITN modified method for Tempus. Whole blood samples collected into Tempus vacuette were extracted using ABI Prism 6100 Nucleic Acid PrepStation and using Tempus extraction reagents. The PAXgene whole blood sample were processed using the PAXgene Blood RNA Kit based on the Qiagen method for column purification of nucleic acid.

treatment_protocol: Whole blood from 7 healthy individuals was collected using Li Heparin tubes, and was incubated for 3 hours at room temperature with or without addition of 25 ug/mL of PHA. After incubation, samples were subsequently transferred to either Tempus or PAXgene tubes.


title: Modifed Adenoma2

value: Adenoma

value: PIK3CA E545K overexpression