title: Top2-1_Top1_Ctrlplasmid_2hr_Supercoil_INPUT

source_name: INPUT fraction of Biotin tagged psoralean of top2-1;top1△ control plasmid in GLU at 37 degree for 2hr15mins S Phase


title: WT_Inf1: WT LCMV infected_RNA-Seq_rep1

status: Public on Mar 11 2019

type: SRA

city: Bethesda

first: Stefano

last: Marenco

state: MD

address: Building 10, Room 4N306

country: USA

institute: National Institute of Mental Health

description:
sample name in processed data file:
WT_Inf1

library_source: transcriptomic

data_processing:
RTA 1.18.64 software used for basecalling.
The sequencing reads were trimmed using Trimmomatic (version 0.30), demultiplexing was done using Bcl2fastq 1.8.4, then mapped to hybrid genome of mm10 and LCMV using STAR version 2.5.2b with two-pass alignment option
The mapped reads in the genomic features were counted by RSEM (version 1.2.22)
Genome_build: hybrid genome (GENECODE Mouse (mm10) and Lymphocytic choriomeningitis virus (NC_004291.1))
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each Sample.

molecule: total RNA

organism: Mus musculus

source_name: NK cells

extract_protocol:
Lin-NK1.1+NKp46+ cells were sorted from spleens of naïve and LCMV-Arm infected mice. Total RNA was isolated from sorted cells using TRIzol (Ambion part of Life Technologies) following the manufacturer’s protocols. During RNA isolation, DNase treatment was additionally performed using the RNase-free DNase set (Qiagen). RNA quality was checked using an Agilent 2100 Expert bioanalyzer (Agilent Technologies). RNA quality was reported as a score from 1 to 10, and samples falling below the threshold of 8.0 were omitted from the study. cDNA library preparation involves the removal of ribosomal RNA (rRNA) using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. The RNA is fragmented into small pieces and the cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The resulting double-strand cDNA is used as the input to a standard Illumina library prep with end-repair, adapter ligation and PCR amplification being performed to give you a library that is ready to go to the sequencer. The final purified product is then quantitated by qPCR before cluster generation and sequencing. Paired-end sequencing (2 × 150 bp) of stranded total RNA libraries was performed on one HiSeq run with Illumina HiSeq3000/4000 chemistry pair end sequencing. The samples have 99 to 148 million pass filter reads with a base call quality of above 92% of bases with Q30 and above.
The HiSeq Real Time Analysis software (RTA 1.18) was used for processing image files, the Illumina bcl2fastq1.8.4 was used to demultiplex and convert binary base calls and qualities to fastq format. The sequencing reads were trimmed adapters and low-quality bases using Trimmomatic (version 0.30), the trimmed reads were mapped to mouse reference genome (GRCm38/mm10) and Gencode annotation M9 using STAR (version 2.5) with two-pass alignment option. RSEM (version 1.2.22) was used for transcript quantification.

tag: tissue

value: spleen

tag: cell type

value: natural killer (NK)

tag: phenotype

tag: genotype

value: wildtype

tag: infected with

value: Lymphocytic choriomeningitis virus


title: Top2-1_Top1_Ctrlplasmid_2hr_Supercoil_IP

type: genomic

city: Milano

first: Mohamood Adhil

last: Mohammed Iqbal

state: Lombardia

address: Via Adamello 16

country: Italy

institute: IFOM - The FIRC Institute of Molecular Oncology

description: Control data from naked genomic DNA used to eliminate the false positive binding of BTMP drug

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R array for 16 hours at 42 C in a hybridization oven at 60 rpm

scan_protocol: Arrays were scanned on Affymetrix geneChip Scanner 3000 7G

data_processing:
The CEL files are processed using rMAT R package for normalization, MAT score calculation and calling enriched regions or peaks. The following commands and parameters are used; i) (Normalization) SetNorm = NormalizeProbes(Set, method="MAT", robust=T, all=T, standard=TRUE, verbose=FALSE), where 'Set' is the probe map object created using CEL file and probe annotation file (Sc03b_MR_v04.bpmap) ii) (MAT score calculation) RD = computeMATScore(SetNorm, dMax=300, verbose=FALSE, cName = InputColumnName), iii) (Calling Enriched Region) peak = callEnrichedRegions(RD, dMax=300, dMerge=300, nProbesMin=8, method=method, threshold=1.5, verbose=FALSE)
Bed file containing the enriched regions with respective MAT score and BedGraph file containing the score for short interval bases. Both bed and bedGraph files are generated using rMAT R package and these files are UCSC genome compatible with sacCer3 reference.

label: biotin

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: IP fraction of Biotin tagged psoralean of top2-1;top1 control pasmid expressed in GLU at 37 degree for 2hr15mins S Phase

label_protocol: Both IP and Input samples are amplified by using Whole genome amplificatio ki protocol ( Sigma-Aldrich WGA1-50RXN) pripor to labelling with Biotin-N11-ddATP (1nMole/ul).

growth_protocol: 1X10e7 cells were synchronized at G1 phase using Alpha-factor and cells were harvested for "G1" samples. For "S" phase samples cells were released into fresh medium after washing cells with 2X YP-medium. After 15 mins of the realese from alpha factor arrest cells were harvested for Chip protocols

extract_protocol:
Genomic DNA was isolated from Qiagen Gneomic-tip 100/G (Cat no 13343) & Genomic DNA buffer Set (Cat no 19060). Purified DNA was sheared to an average size of 500 bp by 6X 15-second pulses using a Biorupter sonicator. bTMP was added to purified DNA and incubated in dark for 90 mins and crosslinked with UV at 365nm (800 mJ/cm2). DNA is precipitated using isopropanol and washed with 70% ethannol. Dried Pellate was dissolved in buffer (50mM tris Ph 8.0, 10mM EDTA, 0.1% SDS) and incuabted with Dynabeads MyOne streptavidin (Invitrogen cat no. 65001) overnight at 4C. The beads were washed 2X with each of the following buffers; wash Buffer I (20mM tris-HCL pH 8, 2mM EDTA, 150mM NaCl, 1% triton X, 0.1% SDS), wash buffer II (20mM tris-HCL pH 8, 2mM EDTA, 500mM NaCl, 1% triton X, 0.1% SDS) wash buffer III (250 mM LiCl, 10 mM Tris pH8.0, 0.5% Na deoxycholate, 0.5% NP40, 1mM EDTA) and 1x TE (20 mM Tris pH8.0, 2 mM EDTA). The bTMP-DNA complexes were eluted from the beads in 250 µl elution buffer (95% Formamide, 10mM EDTA ) at 90C for 20 min and eluted samples were cleaned with Qiagen PCR clean up kit. For Input, DNA was isolated with sheared chromatin input (1/100 of the material used for ChIP).
Cells were collected blocked using Sodium Azide (0.1%). bTMP is added and cells were incubated in dark for 90 mins and crosslinked with UV at 365nm (800 mJ/cm2). The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (50mM Hepes KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate) using Zirconia beads. The crosslinked chromatin was sheared to an average size of 500 bp by 6X 15-second pulses using a Biorupter sonicator. The lysate was then centrifuged to remove cell debris. The chromatin fraction is incuabted with Dynabeads MyOne streptavidin (Invitrogen cat no. 65001) overnight at 4C. The beads were washed 2X with each of the following buffers; wash Buffer I (20mM tris-HCL pH 8, 2mM EDTA, 150mM NaCl, 1% triton X, 0.1% SDS), wash buffer II (20mM tris-HCL pH 8, 2mM EDTA, 500mM NaCl, 1% triton X, 0.1% SDS) wash buffer III (250 mM LiCl, 10 mM Tris pH8.0, 0.5% Na deoxycholate, 0.5% NP40, 1mM EDTA) and 1x TE (20 mM Tris pH8.0, 2 mM EDTA). The bTMP-DNA complexes were eluted from the beads in 250 µl elution buffer (95% Formamide, 10mM EDTA ) at 90C for 20 min and eluted samples were cleaned with Qiagen PCR clean up kit. For Input, DNA was isolated with sheared chromatin input (1/100 of the material used for ChIP).

tag: category

value: BTMP DNA-Supercoil

tag: cell cycle

value: S Phase

tag: antibody

value: Dynabeads My One Streptavidin-(Invitrogen)

tag: strain

tag: treatment

value: Glucose

tag: temperature

value: 37 degree for 2hr 15mins


title: KO_UnInf2: Cd47-/- uninfected_RNA-Seq_rep2

description:
sample name in processed data file:
KO_UnInf2

value: uninfected


title: KO_UnInf1: Cd47-/- uninfected_RNA-Seq_rep1

description:
sample name in processed data file:
KO_UnInf1


title: Top2-1_Top1_Ctrlplasmid_1hr_Supercoil_INPUT

source_name: INPUT fraction of Biotin tagged psoralean of top2-1;top1△ control plasmid in GLU at 37 degree for 1hr15mins S Phase

value: 37 degree for 1hr 15mins


title: r4d35

city: London

first: Tobias

last: Warnecke

address: Du Cane Road

country: United Kingdom

institute: Imperial College

description: Total RNA depleted for ribosomal RNA

data_processing:
Basecalls performed using CASAVA 1.8.4
Reads were aligned to NC_002578.1 T.acidophilum genome assembly obtained from ncbi
Transcripts were reconstructed and quantified using Rockhopper (McClure et al. 2013), using a  threshold of 0.9 for 5’ and 3’UTR detection.
Single-end reads were mapped to the T. acidophilum DSM1728 genome using Geneious 11.1.2 aligner.
Differential expression of transcript delineated by RockHopper was assessed using DESeq2
Genome_build: NC_002578.1
Supplementary_files_format_and_content: Results of 5 and 3 prime UTR detection as well as Operon prediction (RockHopper), Pairwise differential expression computed using DEseq2

organism: Thermoplasma acidophilum

source_name: Thermoplasma acidophilum cells

growth_protocol: T. acidophilum strain 122-1B2 was obtained from DSMZ (https://www.dsmz.de/) and cultured using the medium described in (Searcy and Stein 1980), supplemented to a final concentration of 2g/L yeast extract (BD Biosciences). The medium was boiled for five minutes and allowed to cool to 58°C before inoculation. Cultures were incubated at 59°C with shaking (90rpm) in an INFORS Thermotron incubator.

extract_protocol:
Total RNA was extracted using an RNeasy kit (Qiagen) according to manufacturer’s instruction, including DNAse I treatment.
Ribosomal RNAs were depleted using Illumina’s Ribo-Zero rRNA Removal Kit (Bacteria) and RNA libraries prepared using the TruSeq Stranded Total RNA LT Kit

treatment_protocol: Pellets were re-suspended in 500µL RNAlater (Ambion), incubated for one hour at room temperature, pelleted again and snap-frozen.

tag: time

value: 80 hours after inoculation


title: KO_UnInf4: Cd47-/- uninfected_RNA-Seq_rep4

description:
sample name in processed data file:
KO_UnInf4


title: Top2-1_Top1_Ctrlplasmid_1hr_Supercoil_IP

source_name: IP fraction of Biotin tagged psoralean of top2-1;top1△ control pasmid expressed in GLU at 37 degree for 1hr15mins S Phase


title: C6244R+SEL 4h B

type: RNA

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

institute: The Babraham Institute

hyb_protocol: Samples were hybridized to Illumina Whole-Genome Gene Expression HumanHT-12 v4 Chips (Illumina, Eindhoven, Netherlands), washed and analytical probes bound according to manufacturer's instructions.

scan_protocol: Array scanning was performed using BeadArray Reader (Illumina, Eindhoven, Netherlands) and features extracted using Illumina BeadStudio software (Illumina, Eindhoven, Netherlands).

data_processing: The data was filtered using the detection p-value, at a threshold of >half of the sample to have detected signal for the probe to pass to the comparison stage. The data were then transformed using model-based variance-stabilizing transformation (VST) and normalized using quantile normalization, both using the lumi R software package. Differentially expressed genes were identified using limma bioconductor software package based on a moderated t-test.

organism: Homo sapiens

source_name: COLO205 cells

label_protocol: Sample was amplified using Ambion Illumina TotalPrep RNA Amplification Kit and labelled as part of the Illumina Whole-Genome Gene Expression HumanHT-12 v4 Chip Kit (Illumina, Eindhoven, Netherlands) according to manufacturer’s instructions. Using these, mRNA was converted to single-stranded cDNA using a T7 Oligo(dT) primer to synthesize cDNA containing a T7 promoter sequence. Single-stranded cDNA then underwent second-strand synthesis to produce a dsDNA template for transcription, and residual RNA then removed. cDNA was then amplified and labelled to yield biotinylated cRNA. Impurities were then removed from cRNA in preparation for analysis using Illumina Whole-Genome Gene Expression HumanHT-12 v4 chips.

growth_protocol: Human male COLO205 cells (RRID: CVCL_0218) are a colorectal cancer cell line harbouring the driving oncogene BRAFV600E. These cells are sensitive to inhibition of MEK1/2, the immediate targets of BRAFV600E, and we have made derivatives with resistance to the MEK1/2-inhibitor selumetinib (Sel; AZD6244) as described in Little et al., 2011 Sci. Signal. 4, ra17. These selumetinib-resistant COLO205 cells are termed C6244-R cells. COLO205 cells were grown in RPMI 1640 media supplemented with 10% (v/v) fetal bovine serum, penicillin (100 U/mL), streptomycin (100 mg/mL) and 2 mM glutamine (all from Gibco, Thermo Fisher Scientific, Paisley, UK), and C6244-R cells in the same media with addition of 1 µM selumetinib.

extract_protocol: At the of end treatment cells were lysed in TRI reagent (Sigma-Aldrich, Dorset, UK), typically 2 mL per 10 cm dish, and lysates mixed until a homogenous constituency was achieved. Lysates were transferred to sterile RNase free tubes, and 0.1 mL 1-bromo-3-chloropropane added per mL of lysate. The samples were mixed thoroughly and then allowed to stand for 5 min. Tubes were then centrifuged at 12000 x g for 15 min at 4°C, and the upper aqueous phase transferred to a fresh tube. 0.5 mL 2-propanol per mL original lysate was then added, tubes mixed and allowed to stand for 5 min. Samples were then centrifuged at 12000 x g for 10 min at 4°C, and RNA pellets washed with 75% (v/v) ethanol. Pellets were resuspended in RNase free water and RNA concentrations determined with Nanodrop spectrophotometer (Thermo Fisher Scientific, Loughborough, UK). RNA purity and concentration were checked using a Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific, Loughborough, UK) to determine the A260:A280 ratio.

treatment_protocol: COLO205 and C6244-R cells were washed once with complete medium only, and then treated with either DMSO only containing medium or medium with 1 µM selumetinib for the indicated time points.

tag: cell line

value: Selumetinib-resistant COLO205 (C6244-R)

value: Sel-resistant

tag: agent

value: Selumetinib

value: 4 hr


title: r3d3

description: Total RNA depleted for ribosomal RNA

value: 72 hours after inoculation


title: KO_UnInf3: Cd47-/- uninfected_RNA-Seq_rep3

description:
sample name in processed data file:
KO_UnInf3

value: spleen


title: KO_Inf3: Cd47-/- LCMV infected_RNA-Seq_rep3

description:
sample name in processed data file:
KO_Inf3

value: natural killer (NK)


title: C6244R(-) Revertant 0h B

value: Sel-resistant resensitized

value: 0 hr


title: C6244R-SEL 4h B


title: C6244R-SEL 4h A


title: C6244R+SEL 4h C


title: COLO205 4h A

value: Parental


title: r4d1

description: Total RNA depleted for ribosomal RNA

value: 24 hours after inoculation


title: r3d2

description: Total RNA depleted for ribosomal RNA

value: 48 hours after inoculation


title: COLO205 4h B


title: WT_Ctrlplasmid_2hr_Supercoil_INPUT

source_name: INPUT fraction of Biotin tagged psoralean of wt control plasmid in GLU at 37 degree for 2hr15mins S Phase

value: BTMP DNA-Supercoil

value: S Phase

value: Glucose


title: C6244R(-) Revertant 0h C


title: WT_Ctrlplasmid_2hr_Supercoil_IP

source_name: IP fraction of Biotin tagged psoralean of wt control pasmid expressed in GLU at 37 degree for 2hr15mins S Phase

value: Dynabeads My One Streptavidin-(Invitrogen)

value: 37 degree for 2hr 15mins


title: r3d35

description: Total RNA depleted for ribosomal RNA

value: 80 hours after inoculation


title: r3d1

description: Total RNA depleted for ribosomal RNA


title: C6244R 0h C

value: Selumetinib-resistant COLO205 (C6244-R)

value: Sel-resistant


title: KO_Inf1: Cd47-/- LCMV infected_RNA-Seq_rep1

description:
sample name in processed data file:
KO_Inf1

value: Lymphocytic choriomeningitis virus


title: WT_TopAplasmid_1hr_Supercoil_IP

source_name: IP fraction of Biotin tagged psoralean of wt TopA pasmid expressed in GLU at 37 degree for 1hr15mins S Phase

value: 37 degree for 1hr 15mins


title: WT_Ctrlplasmid_1hr_Supercoil_INPUT

source_name: INPUT fraction of Biotin tagged psoralean of wt control plasmid in GLU at 37 degree for 1hr15mins S Phase


title: KO_Inf4: Cd47-/- LCMV infected_RNA-Seq_rep4

description:
sample name in processed data file:
KO_Inf4

value: spleen


title: C6244R+SEL 4h A

value: Selumetinib

value: 4 hr


title: COLO205 4h C


title: r2d35

description: Total RNA depleted for ribosomal RNA


title: C6244R(-) Revertant 0h A

value: Sel-resistant resensitized

value: 0 hr


title: WT_Ctrlplasmid_1hr_Supercoil_IP

source_name: IP fraction of Biotin tagged psoralean of wt control pasmid expressed in GLU at 37 degree for 1hr15mins S Phase


title: KO_Inf2: Cd47-/- LCMV infected_RNA-Seq_rep2

description:
sample name in processed data file:
KO_Inf2

value: natural killer (NK)


title: r2d3

description: Total RNA depleted for ribosomal RNA

value: 72 hours after inoculation


title: C6244R 0h B


title: r2d2

description: Total RNA depleted for ribosomal RNA

value: 48 hours after inoculation


title: r2d1

description: Total RNA depleted for ribosomal RNA

value: 24 hours after inoculation


title: YFP-PPARalpha-S280D2

city: Newark

first: Michinari

last: Nakamura

state: NJ

address: 185 South Orange Ave MSB-I543

department: Cell Biology and Molecular Medicine

institute: Rutgers New Jersey Medical School

description:
GFP_PPWT_PPA_PPD.txt
PPD2_GGCTAC

data_processing:
CLC Genomics Workbench version 8.5 (http:// www.clcbio.com/products/clc-genomics-workbench/; Qiagen) was used for RNA-seq analysis
De-multiplexed fastq files from RNA-Seq libraries were imported into the CLC software. Adaptor sequences and bases with low quality were trimmed and reads were mapped to a reference genome
Read mapping was carried out with the RNA-Seq Analysis Tool of CLC Genomics Workbench. RPKM values were calculated for each gene to quantify absolute expression. Statistical analysis of differentially expressed genes was carried out with the Empirical analysis of Digital Gene Expression data tool in CLC Genomic Workbench."
Genome_build: Rattus norvegicus (assembly Rnor_6.0)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Rattus norvegicus

growth_protocol: H9C2 cells were maintained in DMEM/F-12 supplemented with 10% (v/v) FBS and 1% pen/strep solution at 37 ℃ in a humidified 5% CO2 incubator.

extract_protocol:
Total RNA was isolated from H9C2 cells transduced with the indicated plasmid using TRIzol (Invitrogen).
Total RNA was subjected to two rounds of poly(A) selection using oligo-d(T)25 magnetic beads (New England Biolabs). A paired-end (strand specific) cDNA library was prepared using the NEB Next Ultra-directional RNA-Seq protocol. Briefly, poly(A)+ RNA was fragmented by heating at 94°C for 10 minutes followed by reverse transcription and second strand cDNA synthesis using the reagents provided in the NEB Next kit. End-repaired cDNA was then ligated with double stranded DNA adapters, followed by purification of ligated DNA with AmpureXP beads. cDNA was then amplified by PCR for 15 cycles with a universal forward primer and a reverse primer with bar code.

treatment_protocol: H9C2 cells were transduced with pDC316-YFP-PPARalpha-wild-type (WT), pDC316-YFP-PPARalpha-S280A phospho-resistant mutant, pDC316-YFP-PPARalpha-S280D phospho-mimicking mutant or pDC316-YFP alone for 2 days.

value: PPARalpha-S280D mutant

value: cardiomyoblast cells


title: ChIP-seq: Hmo1tag-Top2-1-Top1-TopAplasmid-protein-Input

description: Log cells from 28 degree moved to 37 degree for 2hr15mins

library_source: genomic

data_processing:
The raw reads were filtered based on the quality value (-q 20 and –p 30) using FASTX Toolkit. The filtered reads were aligned to the reference genome (SacCer 2011) using TMAP aligner. The PCR duplicates were removed from the aligned BAM files using PICARD tools. The BAM files were sorted and indexed for the peak calling using SAMTOOLS. The bedgraph files were generated by comparing bam files of IP and Input (IP read coverage/Input read coverage) result in the ratio for every base across the whole genome using DEEPTOOLS (bamCompare) (Ramirez et al., 2014). Finally, peak calling was performed using MACS with the following parameters (--gsize=1.21e+7 -n ctrl-A -B -p 0.01 --nomodel --extsize 200 --broad)
Genome_build: SacCer2011 fasta and Saccharomyces_cerevisiae.R64-1-1.89 GTF file
Supplementary_files_format_and_content: bedGraph file and bed file

source_name: Saccharomyces cerevisiae

growth_protocol: Cells were grown at 28 C till 8X10e6 cells per ml, then shifted to 37 C for 2hr 15mins.

extract_protocol:
Cells were crosslinked with 1% formaldehyde in culture medium for 30 min at room temperature followed by quenching with 0.125 M glycine for 5 min. Cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (50mM Hepes KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate) using Zirconia beads. Crosslinked chromatin was sheared to an average size of 500 bp by 6X 15-second pulses using a Biorupter sonicator. The lysate was then centrifuged to remove cell debris. The chromatin fraction was incubated with Dynabeads protein G beads (Invitrogen, cat no 10003D) coated with anti-Flag antibody (M2-antiflag, Sigma) overnight at 40C. The immune complexes were washed with the following buffers 2X; Chip-lysis buffer, high-salt lysis buffer (Chip-lysis buffer + 360mM NaCl), Chip-wash buffer (250 mM LiCl, 10 mM Tris pH8.0, 0.5% Na deoxycholate, 0.5% NP40, 1mM EDTA) and 1x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 250 µl elution buffer (1% SDS, 50 mM Tris pH8.0, 10mM EDTA) at 650C for 20 min followed by the addition of proteinase K to 500 µg/ml and overnight incubation at 650C. Input DNA was isolated from sheared chromatin input (1/100 of the material used for ChIP).
IP and Input ChIP-seq libraries were prepared according to the manufacturer protocols for the Ion Proton sequencer (Thermo Fisher Scientific/Life Technologies). Briefly 10ng for ChIP DNA was end repaired and adapter ligated using the KAPA Library Preparation Kit for Ion Torrent™ (KAPABIOSYSTEMS, inc) and adapter barcode Kapa Barcode Adaptors 9-24 . After adapter ligation, each sample was size selected using AMPure XP Bead (Beckman Coulter, inc). An amplification reaction was set up in a final volume of 50ul . A SPRI cleanup with a 1.5X Bead:DNA ratio was performed post amplification and final libraries were eluted in 35ul. Libraries were quantified on Qubit fluorometer with HS DNA (Thermo Fisher Scientific/Life Technologies) and checked for size on an Agilent Bioanalyzer with HS DNA kit (Agilent, Santa Clara, CA). Each size selected library was diluted according to the final concentration of 11 pM and clonally amplified using the Ion Proton™ Hi‑Q™Template Kit (Thermo Fisher Scientific/Life Technologies) with IonOneTouch 2 instrument (Thermo Fisher Scientific/Life Technologies). After emulsion PCR, DNA positive ISPs were recovered and enriched according to standard protocols with the IonOneTouch ES Instrument (Thermo Fisher Scientific/Life Technologies). A sequencing primer was annealed to DNA positive ISPs and the sequencing polymerase bound, prior to loading of ISPs into Ion P1 sequencing chips. Sequencing of the samples was conducted according to the Ion Proton™ Hi-Q  Sequencing Kit Protocol. One P1 sequencing chips with 6 libraries were loaded and run on an Ion Proton sequencer.

value: Hmo1tag;top2-1;top1<delta>, Ecoli TopA expression using plasmid

value: Log Cells


title: r1d35

description: Total RNA depleted for ribosomal RNA

value: 80 hours after inoculation


title: YFP-PPARalpha-S280D1

description:
GFP_PPWT_PPA_PPD.txt
PPD1_TAGCTT


title: ChIP-seq: Hmo1tag-Top2-1-Top1-TopAplasmid-protein-IP


title: YFP-PPARalpha-S280A2

description:
GFP_PPWT_PPA_PPD.txt
PPA2_ACTTGA

value: PPARalpha-S280A mutant


title: r1d3

description: Total RNA depleted for ribosomal RNA


title: YFP-PPARalpha-S280A1

description:
GFP_PPWT_PPA_PPD.txt
PPA1_CAGATC


title: r1d2

description: Total RNA depleted for ribosomal RNA


title: ChIP-seq: Hmo1tag-Top2-1-Top1-Controlplasmid-protein-IP

value: Hmo1tag, Control plasmid expressed


title: ChIP-seq: Hmo1tag-Top2-1-Top1-Controlplasmid-protein-Input


title: r1d1

description: Total RNA depleted for ribosomal RNA


title: YFP-PPARalpha-wild-type2

description:
GFP_PPWT_PPA_PPD.txt
PPWT3_GCCAAT

source_name: YFP-PPARalpha-wild-type

value: PPARalpha-WT


title: B8_FORM

city: Amherst

first: Begum

middle: D.

last: Topcuoglu

state: MA

address: 336 North Pleasant St., Apt:3B

department: Microbiology

institute: University of Massachusetts

description: Methanocaldococcus jannaschii and Thermococcus paralvinellae

data_processing:
Basecalls performed using Illumina CASAVA software
Sequenced reads were trimmed for adaptor sequence
Reads were mapped to both M. jannaschii and T. paralvinellae genomes using BBSplit from BBMap package (https://sourceforge.net/projects/bbmap/). BBSplit is an aligner tool that bins sequencing reads by mapping to them multiple references simultaneously and separates the reads that map to multiple references to a special "ambiguous" file for each of them
For further analyses we removed all ambiguously mapped reads to both genomes and worked with only the reads that unambiguously map to M. jannaschii genome
The mapped reads for M. jannaschii were aligned to the M. jannaschii genome and sorted using the STAR aligner version 2.5.1b (Dobin et al., 2013). Aligned sequence reads were assigned to genomic features and quantified using featureCounts read summarization tool (Liao et al., 2014)
Genes that were differentially expressed were identified using ‘DESeq2’ in the Bioconductor software framework (www.bioconductor.org) in R (version 3.3 [http://www.r-project.org]) and on a Galaxy platform, respectively (Anders et al., 2010; Goecks et al., 2010; Phipson et al., 2016). RLE (relative log expression)-normalization was performed by using the R package ‘DESeq2’.
Genome_build: M.jannaschii(genome assembly GCA_000091665.1 ASM9166v1) and T.paralvinellae(genome assembly  GCA_000517445.1 ASM51744v1)
Supplementary_files_format_and_content: Tab-delimited text files include RLE-normalized counts for features of interest used in the manuscript. File "DEG_CoCulturesMonoCultures_NormCounts.txt" has all the genes that were differentially expressed (adjusted p-value<0.01 and FoldChange>2) in M. jannaschii when they were grown in coculture compared to monoculture. File "DEG_HighLow_NormCounts" has all the genes that were differentially expressed (adjusted p-value<0.01 and FoldChange>2) in M. jannaschii when they were grown in monoculture under H2 compared to monoculture low H2.
Supplementary_files_format_and_content: raw_counts_unambiguous_afterFeatureCounts.txt

organism:
Methanocaldococcus jannaschii
Thermococcus paralvinellae

source_name: Hyperthermophilic archaea coculture

extract_protocol:
Cell pellets were resuspended in TRIzol (Invitrogen) and total RNA was extracted using a Direct-zol RNA extraction kit (Zymo). RNA quantity was determined with Qubit fluorometry. RNA integrity was checked by a bioanalyzer and a Nanodrop spectrometer. Genewiz sequencing facilities performed rRNA removal, library construction, multiplexing and sequence the RNA with HiSeq2500, 2×100 Paired-End.
RNA libraries were prepared for sequencing using standard Illumina protocols by Genewiz Sequencing Facilities.

tag: culture

value: coculture

tag: carbon source

value: formate

tag: h2 source

value: Thermococcus paralvinellae


title: YFP-PPARalpha-wild-type1

description:
GFP_PPWT_PPA_PPD.txt
PPWT1_TGACCA


title: mouse_macrophage_cell_R264.7_DEX_rep3

city: Philadelphia

first: Hongbo

last: Liu

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: Gene expression after DEX treatment

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Gene Expression 8x60K Microarrays (G4852B) for 17 hours at 10 rpm 65 °C in a rotating Agilent hybridization oven.

scan_protocol: After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) followed by 1 minute with elevated temperature of 37 °C GE Wash buffer 2 (Agilent). Microarrays were scanned immediately on the Agilent DNA Microarray Scanner (G2305C) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: data procsessed by R limma package

source_name: mouse macrophage cell R264.7,DEX treatment,rep3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng total RNA using the One-Color Low Input Quick Amp labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini kit (Qiagen) to purify the labeled, amplified RNA. Dye incorporation and cRNA yield were evaluated with the NanoDrop 2000c Spectrophotometer (Thermo Fisher Scientific).

growth_protocol: RAW264.7 were grow in DMEM medium plus 10% FBS at 37C tissue cultrure incubator with 5% CO2 supply. Cells were splitted in 6 well plate at 0.25 million per well one day before induction.

extract_protocol: Then total RNA were extracted via Qiagen mini RNA extraction kit according to the manuel.

treatment_protocol: When RAW264.7 cells in 6 well plate reach 60% confluence, cells were pretreated with various glucocorticoids (Dexamethasone, VSG158, VSG159, and fluticasone furoate) at 100nM one hour before the onset of inflammation response via LPS at 1 ug/ml for 16 hours.

value: DEX


title: COLO205 0h B

value: Parental

value: 0 hr


title: mouse_macrophage_cell_R264.7_FF_rep3

description: Gene expression after FF treatment

source_name: mouse macrophage cell R264.7,FF treatment,rep3

value: FF


title: COLO205 0h C


title: COLO205 0h A


title: mouse_macrophage_cell_R264.7_VSG159_rep3

description: Gene expression after VSG159 treatment

source_name: mouse macrophage cell R264.7,VSG159 treatment,rep3


title: mouse_macrophage_cell_R264.7_FF_rep2

description: Gene expression after FF treatment

source_name: mouse macrophage cell R264.7,FF treatment,rep2


title: mouse_macrophage_cell_R264.7_FF_rep1

description: Gene expression after FF treatment

source_name: mouse macrophage cell R264.7,FF treatment,rep1


title: mouse_macrophage_cell_R264.7_DEX_rep2

description: Gene expression after DEX treatment

source_name: mouse macrophage cell R264.7,DEX treatment,rep2


title: mouse_macrophage_cell_R264.7_DEX_rep1

description: Gene expression after DEX treatment

source_name: mouse macrophage cell R264.7,DEX treatment,rep1


title: B7_FORM


title: YFP1

description:
GFP_PPWT_PPA_PPD.txt
GFP1_ATCACG

source_name: YFP

value: YFP


title: B3_MAL

value: maltose


title: B4_FORM


title: B6_FORM


title: B2_MAL


title: B1_MAL


title: C42_LOW

organism: Methanocaldococcus jannaschii

source_name: Hyperthermophilic archeaon

value: monoculture


title: mouse_macrophage_cell_R264.7_VSG159_rep2

description: Gene expression after VSG159 treatment

source_name: mouse macrophage cell R264.7,VSG159 treatment,rep2


title: IU1781 WT+TEX-3

city: Houston

first: Nicholas

last: De Lay

state: Texas

address: 6431 Fannin St

department: Microbiology and Molecular Genetics

institute: University of Texas Health Science Center

description: Fragmented rRNA depleted RNA TEX treated

data_processing:
For libararies constructed with Samples 1-6, adapters were trimmed using Cutadapt. Trimmed reads were mapped on the Streptococcus pneumoniae D39 (CP000410.1) genome using Bowtie2 version 2.0.6. Aligned reads were visualized in IGV to identify peaks corresponding to small RNAs.
Read coverage was generated from BAM files using a combination of SAMtools, Bedtools, and a custom R script to normalize coverage per million reads or paired-end fragments. Paired reads were filtered so that only properly-paired reads of fragments less than 600 nt were included in coverage counts.
Genome_build: CP000410.1
Supplementary_files_format_and_content: bigWig files, read coverage maps

organism: Streptococcus pneumoniae D39

source_name: bacterial cells

growth_protocol: Strains were grown in Difco Brain Heart Infusion Broth at 37oC in atmosphere of 5% CO2 to an OD620 of 0.15 to 0.2

extract_protocol:
RNA was isolated from cells via the Fastprep blue kit (MPBiomedicals)
For samples 1-3, the library was generated by removing DNA by DNase treatment, depleting rRNA with Ribo-Zero rRNA removal kit for gram-positive bacteria, fragmenting RNA reagent (Ambion), removing 5' triphosphates via RNA 5' polyphosphatase, and subsequently utilizing the TruSeq Small RNA library kit.  For samples 4-6, the same protocol was used as for Samples 1-3, but prior to RNA 5' polyphosphatase treatment the RNA was treated with Terminator 5'-phosphate-dependent exoribonuclease.

value: TEX

value: wild type


title: C6244R 0h A

source_name: COLO205 cells

value: Selumetinib-resistant COLO205 (C6244-R)

value: Sel-resistant

value: Selumetinib


title: C40_LOW


title: miR-D7-2

city: Beijing

first: Yunfei

last: Zheng

state: Beijing

address: 22 Zhongguancun Avenue South, Haidian District

department: Oral and Maxillofacial Surgery

country: China

institute: Peking University School and Hospital of Stomatology

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

scan_protocol: Scanned on an Agilent G2565CA scanner.

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

source_name: BMSCs D7

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

growth_protocol: BMSCs were cultured in the proliferation medium with 10% FBS and 1% antibiotics.

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

treatment_protocol: BMSCs were cultured in osteogenic medium consisting of α-MEM supplemented with 10%FBS, 1% antibiotics, 100 nM dexamethasone, 0.2 mM ascorbic acid, and 10 mM β-glycerophosphate

tag: tissue

value: Bone marrow-derived mesenchymal stem cells (BMSCs)


title: S_Mf_3

description: Mnase digested DNA

data_processing:
Basecalls performed using CASAVA 1.8.4
Reads were first trimmed with trimgalore to remove adapters and low quality bases.
The trimmed reads were then mapped to the Methanothermus fervidus DSM 2088 genome (GCA_000166095.1) using Bowtie2 (--no-discordant --no-mix). Multimappers were filtered out to retain only reads mapping uniquely.
Coverage tracks were computed using the coverage function in the rtracklayer package for R.
Genome_build: NC_014658.1
Supplementary_files_format_and_content: bigWig

organism: Methanothermus fervidus

source_name: Methanothermus fervidus cells

growth_protocol: Flash-frozen pellets of M. fervidus harvested in late exponential and stationary phase were purchased from the Archaeenzentrum in Regensburg (via Harald Huber).

extract_protocol:
DNA was extracted by phenol chloroform extraction and precipitated with ethanol.
For MNase digestion experiments single-end reads were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina.

treatment_protocol: ~0.5 g of pellet were thawed and resuspended in 9 ml of 1x PBS. Cells were fixed by adding a fixation solution (100mM NaCl, 50mMTris-HCl pH 8.0, 10% formaldehyde) to a final concentration of 1% formaldehyde for 10 minutes (slow rotation) at room temperature. 140mM Glycine for 10 minutes at room temperature (rotating slowly) inhibited formaldehyde and avoided over-fixation. Formaldehyde and glycine residues were washed away by centrifugation (4000 rpm - 5 min - 4C) then bacteria were washed with 10 ml chilled 1x PBS, twice. The archaeal cell pellet was resuspended in 20 ml of chilled 1x PBS. The cell suspension thus obtained was passaged twice through a TS Series French press (Constant Systems) at 15 kpsi and then spun down at 4000 rpm for 15 minutes at 4C before proceeding with cell lysis.The pellet was resuspended in 500 ul of lysis buffer (10mM NaCl, 10mM Tris-HCl pH 7.4, 3mM MgCl2, 0.5% NP-40, 1x Pi, 0.15mM Spermine, 0.5mM Spermidine), transferred in a new microcentrifuge tube and incubated for 20 minutes on ice.  The lysate was spinned down and the pelletwas washed with 500 ul of -CA buffer (15mM NaCl, 10mM Tris-HCl pH 7.4, 60mM KCl, 1x Pi, 0.15mM Spermine, 0.5mM Spermidine) without resuspending. The washed pellet was finally resuspended in 250 ul of +CA Buffer (15mM NaCl, 10mM Tris-HCl pH 7.4, 60mM KCl, 1mM CaCl2,  0.15mM Spermine, 0.5mM Spermidine) to a uniform suspension. 50 ul of this suspension were digested with the wanted concentration of micrococcal nuclease (MN) for 10 minutes (20 minutes for cells in stationary phase) at room temperature and finally blocked with a STOP solution containing calcium-chelating agents (100mM EDTA, 10mM EGTA). Each sample was further diluted with -CA buffer  (without Pi, spermine and spermidine) and treated with 10% SDS and 150ng/ml proteinase K overnight at 65C shaking (~500 rpm).

tag: growth phase

value: stationary phase


title: miR-D0-2

source_name: BMSCs D0


title: S_Mf_2

description: Mnase digested DNA


title: S_Mf_1

description: Mnase digested DNA


title: miR-D0-1


title: mouse_macrophage_cell_R264.7_VSG159_rep1

description: Gene expression after VSG159 treatment

source_name: mouse macrophage cell R264.7,VSG159 treatment,rep1


title: mouse_macrophage_cell_R264.7_VSG158_rep3

description: Gene expression after VSG158 treatment

source_name: mouse macrophage cell R264.7,VSG158 treatment,rep3


title: mouse_macrophage_cell_R264.7_VSG158_rep2

description: Gene expression after VSG158 treatment

source_name: mouse macrophage cell R264.7,VSG158 treatment,rep2


title: mouse_macrophage_cell_R264.7_EtoH_DMSO_rep3

description: Gene expression after EtoH_DMSO treatment

source_name: mouse macrophage cell R264.7,EtoH_DMSO treatment,rep3

value: EtOH, DMSO


title: IU1781 WT+TEX-1


title: IU1781 WT+TEX-2


title: YFP2

description:
GFP_PPWT_PPA_PPD.txt
GFP2_CGATGT

tag: cell type

value: cardiomyoblast cells


title: mouse_macrophage_cell_R264.7_VSG158_rep1

description: Gene expression after VSG158 treatment

source_name: mouse macrophage cell R264.7,VSG158 treatment,rep1


title: Suspended-SPIB-ChIPSeq

city: Tianjin

first: Zhenyi

last: Ma

address: 22 Qixiangtai Road

department: Biochemistry and Molecular Biology

institute: Tianjin Medical University

data_processing:
Basecalling was performed.
SOAPnuke filter used for data filtering
Reads were aligned to the hg38 genome using SOAPaligner/SOAP2 version 2.21t
Peak calling was performed using  macs14
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using macs14

source_name: non-small cell lung cancer cells

growth_protocol: All cells were cultured as protocol on ATCC

extract_protocol:
Lysates were clarified from sonicated nuclei and SPIB-DNA complexes were isolated with antibody.Then DNA fragments were purified with QIAGEN PCR purifiation columns.
DNA was end-repaired,plused A base at 3'end and ligated adapters following Illumina's Paired-End  DNA Sample Prep kit instructions.Then ligated DNA was PCR amplified,denatured and single-chain linked.The purified DNA was performed DNB making and ChIPseq following the manufacturer's protocols.

treatment_protocol: The H1703 cells overexpressing SPIB suspended for 24h

value: lung

value: squamous cell carcinoma cells

tag: chip antibody

value: Monoclonal ANTI-FLAG M2(Sigma, F3165)

tag: condition

value: suspended


title: mouse_macrophage_cell_R264.7_EtoH_DMSO_rep2

source_name: mouse macrophage cell R264.7,EtoH_DMSO treatment,rep2


title: circ-D7-1


title: circ-D0-2


title: E_Mf_4

description: Mnase digested DNA

value: late exponential phase


title: IU1781 WT-TEX-3

description: Fragmented rRNA depleted RNA

tag: genotype


title: C35_HIGH

value: 80uM (aq)


title: Suspended-SPIB-input DNA


title: Attached-SPIB-ChIPSeq

value: attached


title: E_Mf_2

description: Mnase digested DNA


title: miR-D7-1


title: circ-D7-2


title: C34_HIGH

value: monoculture


title: E_Mf_1

description: Mnase digested DNA


title: C38_LOW


title: IU1781 WT-TEX-2

description: Fragmented rRNA depleted RNA


title: Attached-SPIB-input DNA


title: C37_HIGH


title: r1_d2_t0

description: Sheared genomic DNA

data_processing:
Basecalls performed using CASAVA 1.8.4
Reads were aligned to NC_002578.1  T.acidophilum genome assembly obtained from ncbi using Bowtie2
Paired-end 100bp reads were first trimmed using BBDuk v37.64 (parameters: ktrim=r, k=21, hdist=1, edist=0, mink=11, qtrim=rl, trimq=30, minlength=10, ordered=t, qin=33) and then merged using BBmerge v37.64 (parameters: mininsert=10, mininsert0=10).
The merged reads were then mapped to the T. acidophilum DSM1728 genome (GCA_000195915.1) using Bowtie2 (-U).
Coverage tracks were computed using deeptools bamCoverage (RPGC normalization, effective genome size: 1564906bp), measuring coverage for reads of sizes 40-65bp and 70-100bp separately. Reads from the sonicated DNA control samples were mapped in paired-end mode. Coverage was computed independently of read size and smoothed over 10kbp to avoid introducing noise from the input into the MNase signal. Genome-wide coverage of MNase-digested samples was then divided by its corresponding undigested DNA sample to remove bias in coverage associated with replication. Lastly, coverage was converted into a Z-score using the scale function in R.
Genome_build: NC_002578.1
Supplementary_files_format_and_content: Detected peaks on normalized coverage files

source_name: Thermoplasma acidophilum cells

extract_protocol:
DNA was extracted by phenol chloroform extraction and precipitated with ethanol.
For MNase digestion experiments paired-end reads were prepared using the NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: T. acidophilum cells self-lyse at pH>6 (Robb et al. 1995). Pellets were therefore directly re-suspended in ice-cold MNase digestion buffer (10mM Tris, 5mM Ca2+, pH8) and homogenized by 20 passages through a Dounce homogenizer, on ice. Unfixed crude lysates were digested in the presence of 4U/mL of MNase (Thermo Fisher) at 37°C. Digestion was stopped by addition of EDTA to a final concentration of 20mM. Samples were incubated for an additional 30min at 37°C in the presence of RNAse A to a final concentration of 0.5mg/mL and then overnight at 65°C in the presence of SDS (1%) and proteinase K (125µg/mL). Undigested lysate was incubated as above but without addition of enzyme. Undigested DNA was then sonicated using a Covaris S220 sonicator with the following settings: peak power: 175, duty: 10, cycle/burst: 200 for 430s (target size: 150bp).

value: 48 hours after inoculation

value: Undigested


title: IU1781 WT-TEX-1

description: Fragmented rRNA depleted RNA

value: wild type


title: mouse_macrophage_cell_R264.7_EtoH_DMSO_rep1

source_name: mouse macrophage cell R264.7,EtoH_DMSO treatment,rep1


title: MZ2P_U2

status: Public on Mar 10 2019

city: Nanjing

first: Lufeng

state: Jiangsu

address: Tongjia Xiang 24

department: School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention

institute: China Pharmaceutical University

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 hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: breast cancer cells

growth_protocol: Cells were cultured in DMEM medium (Gibco, Grand Island, NY, USA) at 37 °C under a humidified atmosphere with 5% CO2, and supplemented with 10% FBS (Gibco), 80 U/ml penicillin, and 0.08 mg/ml streptomycin.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Transcriptional factor six2 or CYP4Z1 3'UTR or CYP4Z2P 3'UTR  was overexpressed in MCF-7 cells by lentivirus infection, and subjected to  deep sequencing, in triplicate, using Illumina HiSeq 2000.

value: Breast cancer cells

value: CYP4Z2P 3'UTR overexpression


title: six2-1_combined

data_processing:
Basecalls performed using bcl2fastq(v2.17.1.14)
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20,pass filter data of fastq format were processed by Cutadapt[1]（version 1.9.1） to be high quality clean data. Use Homer[3](V4.6) to analyze peaks quality control, peaks calling and peaks annotation.
Quality of sequencing data was evaluated by FastQC (v0.10.1).
Reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, bwa (v0.7.5a-r405) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Bowtie2. Peaks were scanned and annotated throughout the entire genome using Homer (v4.6) software.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include PeakID (represents Peak ID), Chr (represents Chromosome ID), Start (represents the starting site of peak), End (represents the end site of peak), Strand (represents character of strand), Peak Score (represents peak score), Focus ratio for transcritptional factors analysis and Annotation.

extract_protocol:
ChIP-DNA was harvested using EZ-Magna ChIP™ A/G Chromatin Immunoprecipitation Kit (cat # 17-10086, Merck).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Transcriptional factor six2  was overexpressed in MCF-7 cells by lentivirus infection, and subjected to  deep sequencing, in triplicate, using Illumina Hiseq X Ten.

value: six2  overexpression

value: six2 (Proteintech, cat#11562-1-AP)


title: Input-2_combined

value: control


title: Input-1_combined


title: six2-2_combined


title: MZ2P_U1


title: MZ1_U1

value: CYP4Z1 3'UTR overexpression


title: MZ1_U2


title: MCF_7_2


title: circ-D0-1

value: Bone marrow-derived mesenchymal stem cells (BMSCs)


title: MCF_7_1


title: M_six2_2

value: six2 overexpression


title: PD018_BCF2R7_RibosomeProfiling

city: New York

first: Peter

last: Sims

address: 3960 Broadway

department: Systems Biology

institute: Columbia University

description: RNA footprint library_Mouse4

data_processing:
Library strategy: Ribosome profiling
Basecalls were performed on-instrument.
Ribosome profiling: Libraries were processed by removing the first 4 and last 10 positions of each sequenced read with fastx-trimmer run with parameters -f 4, -l 40, and -Q33
Ribosome profiling: Trailing adenines (poly-A sequence) were removed with a custom Python script, discarding reads shorter than 25 bases or with internal poly-A stretches greater than 7 bases.
Ribosome profiling and RNA-seq: Libraries were depleted of ribosomal RNA by alignment to annotated rRNA sequences from mm9 with Bowtie2 and discarding aligned reads, allowing alignments to contain a maximum of one mismatch.
Ribosome profiling and RNA-seq: Unaligned reads were retained and aligned to the mm10 assembly of the mouse genome with STAR v2.5 using default parameters. Ribosome profiling: Reads were additionally aligned to the Gencode-annotated transcriptome for mm10 with STAR v2.5 using the parameter --quantmode TranscriptomeSAM.
Ribosome profiling and RNA-seq: Alignments to the exons (RNA-seq only) and coding sequences (CDS, both RNA-seq and ribosome profiling) of genes were counted with the program featureCounts in Subread v1.4.6; Forward-stranded ribosome profiling alignments were counted with the parameters -s 1 and reverse-stranded RNA-seq alignments were counted with -s 2.
Genome_build: mm10
Supplementary_files_format_and_content: Raw count matrix for all annotated genes in all samples. The first row is unique IDs containing both sample name and alignment type (CDS or exon); the first column is  gene names. 'NA' entries represent invalid alignments, e.g. CDS-aligned reads on non-coding genes.

source_name: CAMKIIa-Ribotag mouse Brain

extract_protocol:
Ribosome Profiling: Monosomes were isolated from RNase I-digested brain lysates on a sucrose gradient fractionator. RNA-Seq: Total RNA was isolated from brain lysates using a Qiagen RNeasy kit (cat no. 74104) and ribosomal RNA was depleted using the Ribo-Zero rRNA removal kit from Illumina (Cat no. MRZH11124) according to the manufacturer’s instructions.
Ligation-free ribosome profiling : Ligation-free ribosome profiling libraries were prepared from dephosphorylated foot-prints (~ 28-34 nucleotides in length) using a commercially available kit (SMARTer small RNA-Seq Library Preparation Kit, Clontech, Cat no. 635029) following manufacturer’s instructions.   RNA-Seq library construction : rRNA depleted total RNA samples were converted to a strand-specific sequencing library using the NEBNext® Ultra™ Directional RNA Library Prep Kit from Illumina (Cat no.E7420S).

value: Fmr1X-Y; Rpl22flox/flox;CamKCre+

tag: tissue origin

value: Mouse Brain Cortex

tag: molecule

value: Ribosome-protected RNA footprint


title: M_six2_1


title: PD018_BCF3R5_RibosomeProfiling

description: RNA footprint library_Mouse3

value: Rpl22flox/flox;CamKCre+  (Control)


title: PD014_BCF4R6_RibosomeProfiling

description: RNA footprint library_Mouse10


title: PD010_BCF2R7_RibosomeProfiling

description: RNA footprint library_Mouse2


title: PD014_BCF2R5_RibosomeProfiling

description: RNA footprint library_Mouse9


title: PD010_BCF3R5_RibosomeProfiling

description: RNA footprint library_Mouse1


title: PD028_BC27_RNASeq

description: Total RNA library_Mouse8

data_processing:
Basecalls were performed on-instrument.
Ribosome profiling: Libraries were processed by removing the first 4 and last 10 positions of each sequenced read with fastx-trimmer run with parameters -f 4, -l 40, and -Q33
Ribosome profiling: Trailing adenines (poly-A sequence) were removed with a custom Python script, discarding reads shorter than 25 bases or with internal poly-A stretches greater than 7 bases.
Ribosome profiling and RNA-seq: Libraries were depleted of ribosomal RNA by alignment to annotated rRNA sequences from mm9 with Bowtie2 and discarding aligned reads, allowing alignments to contain a maximum of one mismatch.
Ribosome profiling and RNA-seq: Unaligned reads were retained and aligned to the mm10 assembly of the mouse genome with STAR v2.5 using default parameters. Ribosome profiling: Reads were additionally aligned to the Gencode-annotated transcriptome for mm10 with STAR v2.5 using the parameter --quantmode TranscriptomeSAM.
Ribosome profiling and RNA-seq: Alignments to the exons (RNA-seq only) and coding sequences (CDS, both RNA-seq and ribosome profiling) of genes were counted with the program featureCounts in Subread v1.4.6; Forward-stranded ribosome profiling alignments were counted with the parameters -s 1 and reverse-stranded RNA-seq alignments were counted with -s 2.
Genome_build: mm10
Supplementary_files_format_and_content: Raw count matrix for all annotated genes in all samples. The first row is unique IDs containing both sample name and alignment type (CDS or exon); the first column is  gene names. 'NA' entries represent invalid alignments, e.g. CDS-aligned reads on non-coding genes.

value: Total RNA


title: PD009_BC7_RNASeq

description: Total RNA library_Mouse2


title: PD028_BC20_RNASeq

description: Total RNA library_Mouse5


title: PD028_BC4_RNASeq

description: Total RNA library_Mouse7


title: PD019_BC3_RNASeq

description: Total RNA library_Mouse3


title: PD019_BC4_RNASeq

description: Total RNA library_Mouse4


title: PD009_BC1_RNASeq

description: Total RNA library_Mouse1


title: 2B

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

data_processing:
Raw sequencing intensities were obtained on a NextSeq500 instrument and converted to base calls using bcl2fastq software (Illumina) with adapter trimming
Alignment to miRbase 21 index of hg19 was performed using Shrimp2
Genome_build: hg19
Supplementary_files_format_and_content: A single data matrix of raw count abundance is provided as a comma separated value (CSV) file for the combined set of 19 samples

source_name: Peripheral blood

extract_protocol:
2.5 ml of whole blood was collected into Paxgene RNA preparation tubes and miRNA purified using a Qiagen miRNA purification kit. The yield and quality of the RNA samples was assessed using the Agilent Bioanalyzer prior to library construction.
llumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 250-500 nanograms of total RNA for the construction of sequencing libraries.

value: Peripheral blood

tag: diagnosis

tag: subject


title: 28A


title: 4A


title: 3Bb

value: acute myeloid leukemia


title: 26A


title: 24A


title: 27A


title: 9-biopsy-control-2-1

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

data_processing:
Reads were trimmed to remove adapter sequence and low-quality base calls with Trimmomatic v0.36
Reads were aligned to reference genome GRCh38 using HISAT2 v 2.1.0
Aligned reads were sorted and indexed using samtools v 1.3
Duplicate reads were marked using Picard MarkDuplicates tool v 2.12.2.
Reads per gene per sample were counted using GenomicAlignments v 1.12.2 summarizeAlignments in "Union" mode
Genes whose expression changes were dependent on diet ("treatment") were identified using DESeq2 v 1.10.0 with a model ~ extraction + treatment + patient.group + extraction:treatment
The entire analysis was executed using a single shell script, which is provided as the supplemental file pipeline.sh.
Genome_build: GRCh38.84
Supplementary_files_format_and_content: raw_counts.csv: Comma separated value file containing raw read counts per sample per gene.
Supplementary_files_format_and_content: normalized_counts.csv: Comma separated value file containing read counts after normalization by DESeq2
Supplementary_files_format_and_content: pipeline.sh: Bash shell script containing all steps to run analysis

source_name: Breast cancer from needle biopsy

extract_protocol:
The specimen was placed into  Qiagen All Protect tissue reagent (Qiagen.com)  and delivered to the research laboratory within 2 hours of collection. Total RNA was extracted using RNeasy, Lipid Tissue kit (Qiagen.com).
Illumina TruSeq with RiboZero reduction; 2x50 paired-end RNA-Seq

value: breast cancer

tag: patient

tag: sample

value: biopsy

tag: diet

tag: replicate


title: 25A


title: 5-surgery-walnut-2-1

source_name: Breast cancer from sugically removed tumor

value: surgery

value: walnut


title: 23A


title: 5-biopsy-walnut-2-1


title: 22A


title: PD028_BC2_RNASeq

description: Total RNA library_Mouse6


title: 3-surgery-control-1-1


title: 3-surgery-control-1-2


title: 16A


title: 18A


title: 17A


title: 2A


title: 19A


title: 1-surgery-walnut-1-1


title: 9-surgery-control-2-1


title: 129-biopsy-control-5-1


title: 1-biopsy-walnut-1-1


title: 14A


title: 129-surgery-control-5-1


title: 15A


title: 13A


title: 124-biopsy-control-4-1


title: 124-surgery-control-4-1


title: 11A


title: H2O2  rep2

city: Chengdu

first: Guoyin

last: Huang

state: Sichuan

address: No.24 South Section 1, Yihuan Road

department: College of Life Sciences

institute: Sichuan University

description: Sample name: 22

data_processing:
Raw data were first processed to filter low quality reads (the number of bases with an error rate >1%), reads containing adapters(cutadapt（version 1.2.1) and reads less than 50 bp
After filtered, high-quality sequences (clean data) were spliced to transcript sequences using software Trinity (version r20140717, k-mer 25bp)
The longest transcripts of each gene were extracted as a representative sequence of the gene, called Unigene
The quantitative software RSEM (30) was used to count the number of reads mapped to each transcript and calculate the FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) value for each gene
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

organism: Dunaliella salina

source_name: Microalgae cells

growth_protocol: Dunaliella salina was grown in defined medium under controlled conditions: 25◦C during a 16/8 h light/dark cycle, light density of 8000 lx

extract_protocol:
Algae cells were collected, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The algae cells were collected by centrifuged for 5 min at 5000×g at 4◦C and subjected to different stress treatments. For experimental groups, algae cells were transferred to fresh medium (containing 1.5 M NaCl) with additional 1.5 M NaCl (high salt stress), 1.5 M sorbitol (hypertonic stress) and 0.4 mM H2O2 (oxidative stress), respectively. Algae cells were transferred to fresh medium were used as control group. All samples were cultivated 2 hours prior to cells collection and collected algae cells immediately stored in liquid nitrogen for further analysis.

tag: strain

tag: age

value: 5 days

tag: stress

value: Whole organism


title: Sorbitol   rep3

description: Sample name: 33

value: Sorbitol

tag: tissue


title: Sorbitol   rep2

description: Sample name: 32


title: H2O2  rep1

description: Sample name: 21


title: 3-biopsy-control-1-1

value: control


title: 121-surgery-control-3-1


title: mosquito bite site of mice treated with naive antiserum -2

city: New Haven

first: Ryuta

last: Uraki

state: CT

address: 300 Cedar Street

department: Internal Medicine

institute: Yale School of medicine

data_processing:
All the analysis of RNA-seq data was performed using Partek flow (v7.0). RNA-seq data were trimmed and mapped to a mm10 genome reference using STAR (2.5.0e). The aligned reads were quantified to ENSEMBL transcripts release 91 using the Partek' E/M algorithm and the subsequent steps were performed on gene-level annotation followed by total count normalization. The gene-level data were normalized by dividing the gene counts by total number of reads followed by addition of a small offset (0.001). Differential expression was assessed by fitting the Partek's log-normal model with shrinkage (comparable in performance to limma-trend). Genes having geometric mean below value of 1.0 were filtered out from the analysis. Hierarchal clustering was performed on the genes, which were differentially expressed across the conditions (P value <0.05, fold change > 1.5 for each comparison)
Genome_build: mm10
Supplementary_files_format_and_content: excel file with gene expression matrix

source_name: skin

extract_protocol:
Mice were euthanized and the locations bitten by mosquitoes and naïve skins were punched using a Disposable Biopsy Punch. Total RNA was extracted by the RNeasy Fibrous Tissue Mini Kit (QIAGEN) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: mosquito bites

value: 24 hours post mosquito feedings

value: skin

tag: treatment

value: Naïve antiserum


title: NaCl  rep3

description: Sample name: 13

value: NaCl


title: BC3

city: Hohhot

first: chunyu

last: Niu

address: college of inner mongolia agricultural university ,306 street zhao wu da ,huhhot ,inner mongolia,china

institute: Inner Mongolia Agricultural University

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 ARS-UCD1.2 (GCA_002263795.2) whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: ARS-UCD1.2 (GCA_002263795.2)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for all Sample

organism: Bos taurus

source_name: bovine vaginal infected with lactobacillus

extract_protocol:
Total RNA from untreated and SQ0048strain-treated BVECs was extracted using Trizol reagent (Invitrogen/Thermo Fisher Scientific, Carlsbad, CA, USA) following the manufacturer's instructions. The quantity and purity of total RNA were analyzed using a Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, Santa Clara, CA, USA), yielding RIN scores >7.0. The cDNA libraries were constructed with RNA isolated from BVECs using a TruSeq Stranded mRNA library preparation kit (Illumina, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: bovine vaginal ephithelial cell

tag: treated

value: treated with lactobacillus strain SQ0048


title: BC2


title: Resting skin site of mice treated with naive antiserum -2

value: No feeding


title: BC1


title: NaCl  rep2

description: Sample name: 12


title: NaCl  rep1

description: Sample name: 11


title: Sorbitol   rep1

description: Sample name: 31


title: 121-biopsy-control-3-1


title: 109-surgery-walnut-3-1


title: mosquito bite site of mice treated with naive antiserum -1


title: Control  rep3

description: Sample name: 03

value: Control


title: con2

source_name: bovine vaginal control

value: untreated group


title: mosquito bite site of mice treated with AgBR1 antiserum -2

value: AgBR1 antiserum


title: con1


title: 122-biopsy-walnut-5-1

value: breast cancer

value: biopsy


title: Control  rep2

description: Sample name: 02


title: con3


title: 114-biopsy-walnut-4-1

value: walnut


title: 109-biopsy-walnut-3-1


title: Control  rep1

description: Sample name: 01

value: 5 days


title: mosquito bite site of mice treated with AgBR1 antiserum -1


title: 114-surgery-walnut-4-1

value: surgery


title: H2O2  rep3

description: Sample name: 23

value: Whole organism


title: 122-surgery-walnut-5-1


title: Resting skin site of mice treated with naive antiserum -1


title: LLS_28_FFPE_CRC

status: Public on Mar 09 2019

city: L'Hospitalet de Llobregat

first: Estela

last: Damaso

state: Barcelona

address: Av.Gran Via de l'Hospitalet, 199-203

department: Hereditary Cancer Program

country: Spain

institute: Catalan Institute of Oncology (ICO)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

scan_protocol: HiScan platform (Illumina)

data_processing:
GenomeStudio software (Methylation Module)
normalized Average Beta by BMIQ method (beta mixture quantile dilation, https://www.ncbi.nlm.nih.gov/pubmed/23175756)

label: Cy3, Cy5

source_name: Lynch-like patient. FFPE DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from FFPE samples was extracted using QIAmp DNA FFPE Tissue Kit (Qiagen) and Deparaffinization Solution (Qiagen) according to the manufacturer's instructions

tag: disease state

value: Lynch-like syndrome (LLS)

tag: gender

value: Female

value: FFPE_CRC tissue

tag: age at diagnosis

tag: microsatellite instability

value: NV

tag: braf status

value: WT

tag: other available files from patient

value: LLS_28_Blood; LLS_28_FFPE_normal colon


title: LLS_90_FFPE_CRC

value: Male

value: MSI+


title: LLS_1_FFPE_CRC


title: LLS_121_FFPE_CRC

value: NP


title: LLS_10_FFPE_CRC


title: LLS_70_FFPE_CRC


title: LLS_78_FFPE_normal colon

value: FFPE_normal colon mucosa


title: LLS_8_FFPE_CRC


title: LLS_66_FFPE_CRC


title: LLS_114_FFPE_CRC


title: LLS_114_FFPE_normal colon

value: LLS_114_Blood; LLS_114_FFPE_CRC


title: LLS_80_FFPE_CRC


title: LLS_83_FFPE_normal colon

value: LLS_83_Blood; LLS_83_FFPE_CRC


title: LLS_116_FFPE_normal colon


title: LLS_50_FFPE_CRC

value: LLS_50_Blood; LLS_50_FFPE_normal colon


title: LLS_5_FFPE_CRC

value: LLS_5_Blood; LLS_5_FFPE_normal colon


title: LLS_75_FFPE_CRC

value: LLS_75_Blood; LLS_75_FFPE_normal colon


title: LLS_6_FFPE_CRC


title: LLS_63_FFPE_CRC


title: LLS_64_FFPE_CRC

value: LLS_64_Blood; LLS_64_FFPE_normal colon


title: LLS_121_FFPE_normal colon

value: LLS_121_Blood; LLS_121_FFPE_CRC


title: LLS_67_FFPE_CRC

value: Lynch-like syndrome (LLS)


title: LLS_108_FFPE_CRC

value: Female


title: LLS_75_FFPE_normal colon

value: LLS_75_Blood; LLS_75_FFPE_CRC


title: LLS_88_FFPE_CRC

value: FFPE_CRC tissue


title: LLS_9_FFPE_CRC

value: WT


title: LLS_113_FFPE_normal colon


title: LLS_83_FFPE_CRC

value: LLS_83_Blood; LLS_83_FFPE_normal colon


title: LLS_27_FFPE_CRC

value: NV


title: LLS_65_FFPE_normal colon

value: Male


title: LLS_64_FFPE_normal colon

value: LLS_64_Blood; LLS_64_FFPE_CRC


title: LLS_61_FFPE_normal colon

value: FFPE_normal colon mucosa


title: LLS_47_FFPE_normal colon


title: LLS_50_FFPE_normal colon

value: LLS_50_Blood; LLS_50_FFPE_CRC


title: LLS_28_FFPE_normal colon

value: LLS_28_Blood; LLS_28_FFPE_CRC


title: LLS_31_FFPE_normal colon


title: LLS_119_Blood

source_name: Lynch-like patient. Genomic DNA

extract_protocol: Genomic DNA was extracted and purified from blood samples using Wizard Genomic DNA Purification Kit  (Promega) according to standard instructions.

value: blood

tag: clinical criteria

tag: personal history of cancer

value: EC

value: MSI+

value: NP


title: LLS_5_FFPE_normal colon

value: LLS_5_Blood; LLS_5_FFPE_CRC


title: LLS_121_Blood

value: Lynch-like syndrome (LLS)

value: AP

value: CRC


title: LLS_123_Blood


title: LLS_110_Blood


title: LLS_107_Blood

value: Female


title: LLS_115_Blood

value: A

value: BC


title: LLS_114_Blood

value: CRC (x2)


title: LLS_104_Blood


title: LLS_105_Blood


title: LLS_98_Blood

value: OC


title: LLS_92_Blood


title: LLS_111_Blood

value: CRC (x2); EC

value: MSS


title: LLS_112_Blood

value: Male

value: NV


title: LLS_96_Blood

value: blood

value: WT


title: LLS_113_Blood

value: MSI+

value: LLS_113_FFPE_normal colon;


title: LLS_102_Blood

value: NP


title: LLS_97_Blood

value: Lynch-like syndrome (LLS)


title: LLS_108_Blood

value: CRC; CRC

value: MSI+/MSS


title: LLS_91_Blood

value: AP

value: CRC


title: LLS_103_Blood

value: Female


title: LLS_116_Blood

value: LLS_116_FFPE_normal colon;


title: LLS_90_Blood


title: LLS_101_Blood


title: LLS_95_Blood


title: LLS_94_Blood


title: LLS_88_Blood


title: LLS_81_Blood


title: LLS_89_Blood


title: LLS_85_Blood

value: GC


title: LLS_82_Blood

value: A

value: OC


title: LLS_86_Blood


title: LLS_84_Blood

value: Male


title: LLS_78_Blood

value: LLS_78_FFPE_normal colon;


title: LLS_80_Blood

value: blood


title: LLS_77_Blood

value: MSS


title: LLS_79_Blood

value: MSI+


title: LLS_74_Blood


title: LLS_62_Blood


title: LLS_70_Blood


title: LLS_73_Blood

value: EC; CRC


title: LLS_69_Blood

value: NP


title: LLS_68_Blood

value: Lynch-like syndrome (LLS)


title: LLS_83_Blood


title: LLS_71_Blood


title: LLS_75_Blood


title: LLS_76_Blood

value: EC; BC


title: LLS_60_Blood


title: LLS_65_Blood

value: LLS_65_FFPE_normal colon;


title: LLS_58_Blood

value: CRC; CRC


title: LLS_64_Blood

value: CRC; CRC; BC


title: LLS_59_Blood

value: CRC


title: LLS_63_Blood

value: Female


title: LLS_72_Blood

value: AP


title: LLS_61_Blood

value: A

value: LLS_61_FFPE_normal colon;


title: LLS_55_Blood

value: Male

value: WT


title: LLS_67_Blood

value: blood


title: LLS_56_Blood


title: LLS_57_Blood

value: OC


title: LLS_53_Blood

value: CRC; CRC (x2)

value: MSI+


title: LLS_54_Blood


title: LLS_66_Blood

value: NP


title: LLS_51_Blood

value: Lynch-like syndrome (LLS)

value: EC


title: LLS_48_Blood


title: LLS_49_Blood

value: CRC; EC


title: LLS_47_Blood

value: LLS_47_FFPE_normal colon;


title: LLS_41_Blood


title: LLS_43_Blood


title: LLS_39_Blood

value: NV


title: LLS_50_Blood

value: CRC


title: LLS_31_Blood

value: Female

value: LLS_31_FFPE_normal colon;


title: LLS_42_Blood


title: LLS_44_Blood


title: LLS_37_Blood

value: AP


title: LLS_52_Blood


title: LLS_40_Blood


title: LLS_45_Blood

value: A


title: LLS_28_Blood


title: LLS_30_Blood

value: Male

value: CRC; CRC

value: NP; MSI+


title: LLS_34_Blood

value: blood

value: Unknown

value: Unkown


title: LLS_46_Blood

value: MSI+

value: WT


title: LLS_36_Blood

value: Lynch-like syndrome (LLS)


title: LLS_33_Blood


title: LLS_38_Blood

value: NP


title: LLS_24_Blood


title: LLS_27_Blood


title: LLS_32_Blood


title: LLS_26_Blood


title: LLS_25_Blood


title: LLS_23_Blood


title: FUSCCTNBC471_FrozenPrimaryTumorTissue

city: Shanghai

first: Zhi-Ming

last: Shao

address: 270 Dong An Road, Build 7, RM304

institute: Fudan University Shanghai Cancer Center

description: Copy number profiling of patient FUSCCTNBC471, fresh frozen primary tumor tissue

hyb_protocol: Genome-wide copy number analysis was performed using an OncoScan CNV Assay Kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s recommendations. Briefly, a total of 80 ng of DNA from each tumor sample was processed. Molecular inversion probes (MIPs) were added to the sample DNA and annealed at 58°C overnight. The annealed DNA was divided into two equal parts and incubated with AT or GC gap-fill master mixes for ligation. Then, the unincorporated, non-circularized MIPs and the remains of the genomic template were removed through exonuclease treatment. The circularized MIPs were linearized with a cleavage enzyme, and the first PCR amplification was performed, followed by a second amplification. The amplified products were digested with HaeIII, and the small fragments containing the specific SNP genotype were hybridized onto arrays.

scan_protocol: The arrays were washed and stained using GeneChip Fluidics Station 450 (Affymetrix, Inc.) and scanned in GeneChip Scanner 3000 7G (Affymetrix, Inc.). The fluorescence of clusters was measured to generate a DAT file. Cluster intensity values were automatically calculated using a built-in algorithm from DAT files using GeneChip Command Console software (Affymetrix, Inc.), and a CEL file was generated.

data_processing:
An analysis of Affymetrix OncoScan CNV SNP probe assays was performed with OncoScan Console (v1.3) software (Affymetrix, Inc.). BioDiscovery Nexus ExpressTM for OncoScan 3 software was used to assess recurrent germline/potential false-positive calls by using a reference cohort of DNA from 23 white blood cell samples (regions altered in 12 or more patients were defined as recurrent germline/potential false-positive calls which would be removed later).  Probe-level output from OncoScan Console were analyzed using ASCAT (v2.4.2)(Van Loo et al., 2010) to obtain segmented copy number calls, estimated tumor ploidy as well as estimated tumor purity.
Primary data description: Output (probe level) of OncoScan Console (v1.3): Log2Ratio, WeightedLog2Ratio, AllelicDifference, NormalDiploid, BAF (B allele frequency)

source_name: Patient FUSCCTNBC471 fresh frozen primary tumor tissue

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Tumor tissues were macrodissected to avoid the influence of stromal tissues (< 10% stromal). The percentage of tumor cells was confirmed to be 50% or more in all the breast cancer specimens. Total DNA was isolated from 485 fresh frozen TNBC samples using TGuide M24 (Tiangen, Beijing, China). The purity and quantity of total DNA were estimated by measuring absorbance at 260 nm (A260) and 280 nm (A280) using a NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). The extracted DNA was considered pure and suitable for future experiments when the A260/A280 ratio was within 1.6-1.9

tag: patient id

value: Primary triple negative breast cancer


title: FUSCCTNBC467_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC467, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC467 fresh frozen primary tumor tissue


title: LLS_21_Blood


title: LLS_29_Blood


title: FUSCCTNBC465_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC465, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC465 fresh frozen primary tumor tissue


title: FUSCCTNBC464_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC464, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC464 fresh frozen primary tumor tissue


title: FUSCCTNBC461_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC461, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC461 fresh frozen primary tumor tissue


title: LLS_19_Blood


title: FUSCCTNBC456_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC456, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC456 fresh frozen primary tumor tissue


title: FUSCCTNBC454_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC454, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC454 fresh frozen primary tumor tissue


title: FUSCCTNBC453_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC453, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC453 fresh frozen primary tumor tissue


title: FUSCCTNBC451_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC451, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC451 fresh frozen primary tumor tissue


title: LLS_20_Blood


title: FUSCCTNBC449_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC449, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC449 fresh frozen primary tumor tissue


title: FUSCCTNBC448_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC448, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC448 fresh frozen primary tumor tissue


title: FUSCCTNBC447_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC447, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC447 fresh frozen primary tumor tissue


title: FUSCCTNBC452_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC452, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC452 fresh frozen primary tumor tissue


title: LLS_18_Blood


title: FUSCCTNBC446_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC446, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC446 fresh frozen primary tumor tissue


title: FUSCCTNBC444_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC444, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC444 fresh frozen primary tumor tissue


title: FUSCCTNBC445_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC445, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC445 fresh frozen primary tumor tissue


title: FUSCCTNBC443_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC443, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC443 fresh frozen primary tumor tissue


title: LLS_16_Blood

source_name: Lynch-like patient. Genomic DNA


title: LLS_22_Blood


title: FUSCCTNBC441_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC441, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC441 fresh frozen primary tumor tissue


title: FUSCCTNBC440_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC440, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC440 fresh frozen primary tumor tissue


title: FUSCCTNBC437_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC437, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC437 fresh frozen primary tumor tissue


title: FUSCCTNBC442_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC442, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC442 fresh frozen primary tumor tissue


title: FUSCCTNBC436_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC436, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC436 fresh frozen primary tumor tissue


title: LLS_12_Blood


title: LLS_14_Blood


title: FUSCCTNBC438_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC438, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC438 fresh frozen primary tumor tissue


title: FUSCCTNBC457_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC457, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC457 fresh frozen primary tumor tissue


title: LLS_8_Blood


title: LLS_11_Blood

value: SBC


title: LLS_17_Blood

value: CRC


title: LLS_10_Blood


title: FUSCCTNBC429_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC429, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC429 fresh frozen primary tumor tissue


title: FUSCCTNBC435_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC435, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC435 fresh frozen primary tumor tissue


title: FUSCCTNBC434_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC434, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC434 fresh frozen primary tumor tissue


title: FUSCCTNBC432_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC432, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC432 fresh frozen primary tumor tissue


title: FUSCCTNBC425_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC425, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC425 fresh frozen primary tumor tissue


title: FUSCCTNBC431_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC431, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC431 fresh frozen primary tumor tissue


title: FUSCCTNBC430_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC430, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC430 fresh frozen primary tumor tissue


title: FUSCCTNBC427_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC427, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC427 fresh frozen primary tumor tissue


title: FUSCCTNBC428_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC428, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC428 fresh frozen primary tumor tissue


title: FUSCCTNBC458_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC458, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC458 fresh frozen primary tumor tissue


title: LLS_9_Blood

source_name: Lynch-like patient. Genomic DNA

value: Female


title: LLS_35_Blood


title: LLS_4_Blood


title: LLS_3_Blood


title: FUSCCTNBC421_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC421, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC421 fresh frozen primary tumor tissue


title: LLS_2_Blood


title: FUSCCTNBC420_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC420, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC420 fresh frozen primary tumor tissue


title: FUSCCTNBC416_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC416, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC416 fresh frozen primary tumor tissue


title: FUSCCTNBC414_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC414, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC414 fresh frozen primary tumor tissue


title: LLS_15_Blood


title: FUSCCTNBC415_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC415, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC415 fresh frozen primary tumor tissue


title: LLS_6_Blood


title: FUSCCTNBC413_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC413, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC413 fresh frozen primary tumor tissue


title: LLS_1_Blood


title: FUSCCTNBC401_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC401, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC401 fresh frozen primary tumor tissue


title: FUSCCTNBC405_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC405, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC405 fresh frozen primary tumor tissue


title: FUSCCTNBC403_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC403, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC403 fresh frozen primary tumor tissue


title: FUSCCTNBC402_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC402, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC402 fresh frozen primary tumor tissue


title: FUSCCTNBC426_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC426, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC426 fresh frozen primary tumor tissue


title: FUSCCTNBC407_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC407, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC407 fresh frozen primary tumor tissue


title: FUSCCTNBC412_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC412, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC412 fresh frozen primary tumor tissue


title: LLS_5_Blood

value: LLS_5_FFPE_normal colon; LLS_5_FFPE_CRC


title: LLS_13_Blood


title: FUSCCTNBC400_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC400, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC400 fresh frozen primary tumor tissue


title: FUSCCTNBC404_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC404, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC404 fresh frozen primary tumor tissue


title: FUSCCTNBC423_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC423, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC423 fresh frozen primary tumor tissue


title: FUSCCTNBC422_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC422, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC422 fresh frozen primary tumor tissue


title: FUSCCTNBC399_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC399, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC399 fresh frozen primary tumor tissue


title: FUSCCTNBC398_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC398, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC398 fresh frozen primary tumor tissue


title: FUSCCTNBC406_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC406, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC406 fresh frozen primary tumor tissue


title: FUSCCTNBC397_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC397, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC397 fresh frozen primary tumor tissue


title: FUSCCTNBC395_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC395, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC395 fresh frozen primary tumor tissue


title: FUSCCTNBC393_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC393, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC393 fresh frozen primary tumor tissue


title: FUSCCTNBC394_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC394, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC394 fresh frozen primary tumor tissue


title: FUSCCTNBC392_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC392, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC392 fresh frozen primary tumor tissue


title: FUSCCTNBC390_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC390, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC390 fresh frozen primary tumor tissue


title: FUSCCTNBC389_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC389, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC389 fresh frozen primary tumor tissue


title: FUSCCTNBC387_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC387, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC387 fresh frozen primary tumor tissue


title: FUSCCTNBC386_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC386, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC386 fresh frozen primary tumor tissue


title: FUSCCTNBC385_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC385, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC385 fresh frozen primary tumor tissue


title: FUSCCTNBC384_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC384, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC384 fresh frozen primary tumor tissue


title: FUSCCTNBC391_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC391, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC391 fresh frozen primary tumor tissue


title: FUSCCTNBC381_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC381, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC381 fresh frozen primary tumor tissue


title: FUSCCTNBC380_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC380, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC380 fresh frozen primary tumor tissue


title: FUSCCTNBC377_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC377, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC377 fresh frozen primary tumor tissue


title: FUSCCTNBC382_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC382, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC382 fresh frozen primary tumor tissue


title: FUSCCTNBC376_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC376, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC376 fresh frozen primary tumor tissue


title: FUSCCTNBC374_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC374, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC374 fresh frozen primary tumor tissue


title: FUSCCTNBC375_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC375, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC375 fresh frozen primary tumor tissue


title: FUSCCTNBC383_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC383, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC383 fresh frozen primary tumor tissue


title: FUSCCTNBC373_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC373, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC373 fresh frozen primary tumor tissue


title: FUSCCTNBC372_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC372, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC372 fresh frozen primary tumor tissue


title: FUSCCTNBC371_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC371, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC371 fresh frozen primary tumor tissue


title: FUSCCTNBC370_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC370, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC370 fresh frozen primary tumor tissue


title: FUSCCTNBC368_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC368, peripheral white blood cell

source_name: Patient FUSCCTNBC368 peripheral white blood cell

value: Peripheral white blood cell


title: FUSCCTNBC369_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC369, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC369 fresh frozen primary tumor tissue


title: FUSCCTNBC376_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC376, peripheral white blood cell

source_name: Patient FUSCCTNBC376 peripheral white blood cell


title: FUSCCTNBC366_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC366, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC366 fresh frozen primary tumor tissue


title: FUSCCTNBC368_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC368, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC368 fresh frozen primary tumor tissue


title: FUSCCTNBC362_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC362, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC362 fresh frozen primary tumor tissue


title: FUSCCTNBC365_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC365, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC365 fresh frozen primary tumor tissue


title: FUSCCTNBC361_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC361, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC361 fresh frozen primary tumor tissue


title: FUSCCTNBC360_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC360, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC360 fresh frozen primary tumor tissue


title: FUSCCTNBC356_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC356, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC356 fresh frozen primary tumor tissue


title: FUSCCTNBC354_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC354, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC354 fresh frozen primary tumor tissue


title: FUSCCTNBC353_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC353, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC353 fresh frozen primary tumor tissue


title: FUSCCTNBC359_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC359, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC359 fresh frozen primary tumor tissue


title: FUSCCTNBC357_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC357, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC357 fresh frozen primary tumor tissue


title: FUSCCTNBC350_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC350, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC350 fresh frozen primary tumor tissue


title: FUSCCTNBC346_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC346, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC346 fresh frozen primary tumor tissue


title: FUSCCTNBC352_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC352, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC352 fresh frozen primary tumor tissue


title: FUSCCTNBC345_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC345, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC345 fresh frozen primary tumor tissue


title: FUSCCTNBC344_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC344, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC344 fresh frozen primary tumor tissue


title: FUSCCTNBC347_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC347, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC347 fresh frozen primary tumor tissue


title: FUSCCTNBC348_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC348, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC348 fresh frozen primary tumor tissue


title: FUSCCTNBC351_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC351, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC351 fresh frozen primary tumor tissue


title: FUSCCTNBC343_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC343, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC343 fresh frozen primary tumor tissue


title: FUSCCTNBC344_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC344, peripheral white blood cell

source_name: Patient FUSCCTNBC344 peripheral white blood cell


title: FUSCCTNBC424_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC424, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC424 fresh frozen primary tumor tissue


title: FUSCCTNBC339_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC339, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC339 fresh frozen primary tumor tissue


title: FUSCCTNBC336_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC336, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC336 fresh frozen primary tumor tissue


title: FUSCCTNBC364_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC364, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC364 fresh frozen primary tumor tissue


title: FUSCCTNBC340_WhiteBloodCell

description: Copy number profiling of patient FUSCCTNBC340, peripheral white blood cell

source_name: Patient FUSCCTNBC340 peripheral white blood cell


title: FUSCCTNBC338_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC338, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC338 fresh frozen primary tumor tissue


title: FUSCCTNBC333_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC333, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC333 fresh frozen primary tumor tissue


title: FUSCCTNBC332_FrozenPrimaryTumorTissue

description: Copy number profiling of patient FUSCCTNBC332, fresh frozen primary tumor tissue

source_name: Patient FUSCCTNBC332 fresh frozen primary tumor tissue