title: AX7894 d4_1

city: Klosterneuburg

first: Giulio

last: Valperga

address: Am Campus 1

country: Austria

institute: IST Austria

description:
Library was sequecned twice. There are two sequencing file for each sample.
qui-1.rep4

data_processing:
Data quality was checked using FastQC 0.11.7, before and after adaptor clipping
Trimming quality was controlled using trimmomatic 0.38
Cleaned data were used for gene quantification using Salmon 1.1.0, C. elegans transcriptome (EnsemblMetazoa: release 46)
Differential gene expression analysis was performed using tximport 1.14.2 and DEseq2 1.26.0
Genome_build: C. elegans transcriptome (EnsemblMetazoa: release 46) and C. elegans genome (WBcel235) as decoy
Supplementary_files_format_and_content: Excel file. The file contains raw count, normilised transcript per million (tpm) for each gene in the C. elegans genome in both wild type and qui-1 condition. For each gene an average of its expression levels (tpm) in wild type and qui-1 sample is reported as well as annotation of its neural function (See Hobert, 2006; Robertson and Thomas, 2006) and protein function (Uniprot). For each gene the fold change between its expression in wild type and qui-1 is reported (log2(FC)), including statistcs as computed by DEseq2 (p-value,q-value).

organism: Caenorhabditis elegans

source_name: FACSorted mKate positive neurons

growth_protocol: Animals were grown on standard NGM plates seeded with OP50 at least 3 days before. Animals were grown at room temperature.

extract_protocol:
Synchronised transgenic young adults in which the ADL neurons were specifically labelled using srh-220p:mKate2 were washed 5x in M9 Buffer to remove bacteria and then dissociated as described (Beets et al., 2020; Kaletsky et al., 2018). Briefly, animals were incubated for 6.5 min in Lysis Buffer (200mM DTT, 0.25% SDS, 20mM HEPES, 3% sucrose) washed 5x in M9 Buffer, resuspended in 500 μL of 20 mg/uL Pronase in water, and pipetted up and down for 12 min at room temperature. The reaction was stopped by adding 250 μl of 2% FBS in PBS. Cells were filtered through a 5 μm syringe filter to remove clumps. mKate positive cells were sorted using a Synergy High Speed Cell Sorter (Sony Biotechnology) with gates set using a negative control prepared in parallel from dissociated unlabelled N2 animals. Positive cells were collected into 10 μL of Triton X-100 0.2% (vol/vol) supplemented with 2U/mL RNase inhibitors. Between 700 and 3000 cells were collected for each biological replicate.
Library preparation of sorted neurons was adapted from Picelli et al., . Briefly, fluorescently-labelled neurons collected by FACS were lysed in 10 μL of 0.2% Triton X-100 (vol/vol) and 2U/μL RNase inhibitors. The reverse transcription reaction volumes were adjusted to a 10 μL input and cDNA prepared using oligo dT primers and template-switching oligos (TSO) to enrich for polyadenylated transcripts and allow for pre-amplification of cDNA. cDNA was pre-amplified using custom PCR primers. 50 μL of PCR product from the pre-amplification step were purified using 50 μL of Ampure XP beads (Beckman Coulter), resuspended, and used at a concentration of 0.2 ng/uL as input for library preparation using the Nextera XT DNA Kit. Library preparation followed the manufacturer’s instruction. The quality of RNAseq libraries was assessed on a Bioanalyzer (Agilent) using High Sensitivity Gels (Agilent). Library concentration was measured using a Qubit dsDNA High Sensitivity Kit (Thermo Fisher Scientific) and sequenced on the Illumina HiSeq 4000 platform.

tag: age

value: day 1 adult animals

value: db104 mutant allele (qui-1)


title: adipose tissue, patient  1

status: Public on Mar 10 2021

type: RNA

city: Milano

first: Stefano

last: Percio

state: Milano

address: Via Amadeo 42

department: DRAST

country: Italy

institute: Fondazione IRCCS - Istituto Nazionale dei Tumori

description: gene expression data from retroperitoneal liposarcoma patient

hyb_protocol: Hybridization was performed according to manufacturer's standard protocols.

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

data_processing: Arrays were RMA normalized (Irizarry et al. 2003) and differential expression determined using the following R packages from the Bioconductor project: oligo (Carvalho et al. 2010), limma (Smyth 2004).

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: adipose tissue

label_protocol: RNA was labeled and processed according to manufacturer's recommended protocols.

extract_protocol: RNA was extracted from snap-frozen tissues using Qiagen RNeasy kit purification performed according to the manufacturer's instructions.

tag: tissue

value: adipose tissue


title: DHA3

type: SRA

city: Bethesda

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

country: USA

institute: NIH

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed using trimgalore
The trimmed reads were aligned tomouse (hg38) genome using HISAT2 align with parameters --no-mixed --no-discordant.
Aligned reads were transformed into .bam files and sorted by coordinate using sambamba view and sambamba sort.
Read counts were generated using the featureCounts program from the subread package.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes reads counts  for each sample

source_name: Primary Hepatocyte

growth_protocol: The cryopreserved primary human hepatocytes were obtained from Thermo Fisher Scientific. Manufacture’s recommendations were followed when culturing of primary human hepatocytes. Specifically, hepatocytes were thawed, pelleted, resuspended with plating medium (William’s medium E supplemented with Hepatocyte Plating Supplement Pack) (Thermo Scientific) and seeded in 24 well plate pre-coated with type I collage at a density of 5x105 cells/ well.

extract_protocol:
Total RNA was isolated from primary human hepatocytes using KingFisher PURE RNA tissue Kit.
RNA libraries were prepared for sequencing using standard Illumina kit and protocols; strand-specific

treatment_protocol: For omega-3 fatty acid treatment, EPA, DHA and OA from Cayman chemical were dissolved in ethanol and further dilute 1:1000 in incubation medium (serum free) containing 1% fatty acid free BSA (Sigma). Overnight plated primary human hepatocytes were cultured in serum free incubation medium, washed and then refed with incubation medium containing 1% fatty acid free BSA and different treatments (ethanol as vehicle or 200M DHA/EPA/OA) for 16 hours before cells were harvested for RNA extraction.

tag: cell type

value: hepatocyte

tag: treatment

value: DHA


title: AX7866 d4_1

description:
Library was sequecned twice. There are two sequencing file for each sample.
WT.rep5

tag: genotype

value: N2 (WT)


title: Sample 8_12_S28_L004

city: Houston

first: xingzhe

last: ma

state: TX

address: 6565 fannin street

department: cancer center

institute: houston methodist hospital

data_processing:
kallisto quant for gene expression quantification
tximport to import and summarize transcript level estimates
DESeq2 to compare abundance and calculate fpkm
Genome_build: GENCODE VM23 (GRCm38.p6)
Supplementary_files_format_and_content: TPM and estimate counts of transcript

organism: Mus musculus

source_name: CD36 KO_B16 tumor infiltrating cd8 t cells

growth_protocol: CD36 KO or C57BL/6 mice were injected i.v. with B16 tumor cells

extract_protocol:
tumors were collected for sorting of CD8 T cells
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: tumors were grown for 14 days

tag: strain background

tag: genotype/variation

value: CD36 KO

value: B16 tumor infiltrating CD8 T cells


title: AX7894 d3_2

description:
Library was sequecned twice. There are two sequencing file for each sample.
qui-1.rep3


title: well differentiated liposarcoma, patient  1

source_name: well differentiated liposarcoma

value: well differentiated liposarcoma


title: S5_HC_H3K9me3

city: Essen

first: Manuela

last: Wuelling

address: Universitätsstrasse 2

department: Developmental Biology

country: Germany

institute: University Duisburg-Essen

library_source: genomic

data_processing:
fastqc (version v0.11.9) > 20
prinseqlite trimming to 60 bp
mapping to mm10 (UCSC, Dec. 2011)
samtool, mapping quality >30
Picard tools, filtering of duplicates
hiddenDomains for peak calling, bin size 200 bp, max. read count 30, p> 0.6, 20 bp for narrow, 800 bp for braod peaks
intersection of conservative peaks  biological replicates
Genome_build: mm10
Supplementary_files_format_and_content: bed files, peak calling with Hidden domain
Supplementary_files_format_and_content: bed files of the intersection

molecule: genomic DNA

source_name: cartilage from E15.5 mouse embryo

extract_protocol:
proliferating chondrocyte were isolated from E13.5, hypertrophic chondrocytes from E15.5 mouse embryos
cell sorting was perfomred on a FACSAria II cell sorter with a 70 µm nozzle. Chip was isoaled with True MicroChip Kit (Diagenode).
MicroPlex Library preparation Kit V2 (Diagenode)

value: primary hypertrophic chondrocytes

tag: strain

value: cartilage from E15.5 mouse embryo

tag: chip antibody

value: H3K9me3 (Diagenode C1541093)


title: dedifferentiated liposarcoma, patient  16

source_name: dedifferentiated liposarcoma

value: dedifferentiated liposarcoma


title: Sample 7_12_S28_L003


title: adipose tissue, patient  14


title: AX7866 d3_1

description:
Library was sequecned twice. There are two sequencing file for each sample.
WT.rep4


title: dedifferentiated liposarcoma, patient  1


title: well differentiated liposarcoma, patient  14


title: AX7866 d4_2

description:
Library was sequecned twice. There are two sequencing file for each sample.
WT.rep6


title: DHA1


title: Sample 6_12_S28_L002


title: dedifferentiated liposarcoma, patient  14


title: AX7894 d3_1

description:
Library was sequecned twice. There are two sequencing file for each sample.
qui-1.rep2


title: BSA_ethanol5


title: Sample 5_12_S28_L001


title: AX7894 d2_1

description:
Library was sequecned twice. There are two sequencing file for each sample.
qui-1.rep1


title: Sample 4_8_S25_L004

source_name: WT_B16 tumor infiltrating cd8 t cells

value: wild type


title: adipose tissue, patient  13


title: DHA2


title: adipose tissue, patient  16


title: BSA_ethanol4


title: BSA_ethanol3


title: AX7866 d2_1

description:
Library was sequecned twice. There are two sequencing file for each sample.
WT.rep3


title: dedifferentiated liposarcoma, patient  13


title: BSA_ethanol2


title: AX7866 d1_2

description:
Library was sequecned twice. There are two sequencing file for each sample.
WT.rep2


title: Sample 2_8_S25_L002


title: BSA_ethanol1


title: AX7866 d1_1

description:
Library was sequecned twice. There are two sequencing file for each sample.
WT.rep1


title: well differentiated liposarcoma, patient  13


title: adipose tissue, patient  5


title: well differentiated liposarcoma, patient  5


title: USP7-wild-type_1 [Hausp44.wt.wt.S7]

status: Public on Mar 09 2021

city: Memphis

first: Timothy

last: Shaw

state: TN

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hospital

data_processing:
Basecalls performed using CASAVA
fastq files werer mapped by STAR_2.4.1d_modified parameters --chimSegmentMin 20 --chimJunctionOverhangMin 20
reads were counted using htseq/0.6.1p1 with Mus_musculus.NCBIM37.67.gtf
htseq was used to derive the read counts with parameters -r name -a 0 -s no -m union -t exon
Genome_build: mm9
Supplementary_files_format_and_content: counts

source_name: USP7 wild-type in the hematopoeitic system

extract_protocol:
RNA samples were isolated using the RNeasy Mini Kit (QIAGEN)
The total stranded RNA library was prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche Sequencing). RNA sequencing was performed on NovaSeq 6000 system (Illumina).

treatment_protocol: Total RNA was extracted from the thymus 3 days after birth.

value: Thymus

tag: molecule subtype

value: Ribo-depleted


title: Sample 1_8_S25_L001


title: USP7-wild-type_4 [Hausp56.wt.S10]

value: USP7 wild-type in the hematopoeitic system


title: heterozygous_KO-2 [Hausp61.het.S5]

source_name: Heterozygous knock-out of USP7 in the hematopoeitic system


title: homozygous-KO-2 [Hausp57.homo.S2]

source_name: Homozygous knock-out of USP7 in the hematopoeitic system


title: homozygous-KO-3 [Hausp62.homo.S3]

value: Homozygous knock-out of USP7 in the hematopoeitic system


title: USP7-wild-type_3 [Hausp51.wt.S9]


title: homozygous-KO-1 [Hausp50.homo.S1]


title: Sample 3_8_S25_L003


title: NIH/3T3 LSD1 ChIP-seq

city: Stuttgart

first: Philipp

last: Rathert

state: Germany

address: Allmandring 31

department: Biochemistry

institute: University Stuttgart

data_processing:
Paired-end sequence reads were of 150bp in length and mapped to the reference murine genome assembly NCBI37/mm9 using Bowtie2
Peaks were identified using MACS2 (Model based Analysis of ChIP-Seq) peak finding algorithm.
A q-value threshold of enrichment of 0.05 relative to input control samples were used for all peak calling.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated

source_name: cell line

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

value: Fibroblast

value: embryo


title: AH1263_37_B

city: Athens

first: Ronan

middle: Kevin

last: Carroll

state: OHIO

address: 107 Irvine Hall

department: Biological Sciences

institute: Ohio University

description: total RNA, rRNA-depleted

data_processing:
Raw data files (.fastq) were imported into the CLC Genomics Workbench (v11) software platform for analysis
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Replicate data sets were grouped and normalized using "quantile normalization"
Normalized expression values were exported into excel files
Genome_build: The reference genome used for the analysis was based on NC_007793 and included annotations for sRNA genes (https://dx.doi.org/10.6084/m9.figshare.2061132.v1)
Supplementary_files_format_and_content: Expression values for each gene were initially calculated as RPKM values. The RPKM values were then normalized and the "Normalized expression values" are presented in the excel files

organism: Staphylococcus aureus

source_name: Bacterial cells, pelleted

growth_protocol: Strains were grown in TSB medium at 37°C with shaking to an OD600 of approx 6.5

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion DNA-free
Library construction was performed using the Illumina TruSeq Stranded mRNA Sample Prep Kit

treatment_protocol: Samples were stored at -80°C prior to RNA extraction

value: wild-type

tag: growth medium

value: TSB

tag: growth temperature


title: AH1263_40_A

description: total RNA, rRNA-depleted


title: AH1263_37_A

description: total RNA, rRNA-depleted


title: AH1263_40_B

description: total RNA, rRNA-depleted


title: AH1263_40_C

description: total RNA, rRNA-depleted


title: AH1263_34_C

description: total RNA, rRNA-depleted


title: AH1263_34_B

description: total RNA, rRNA-depleted


title: USP7-wild-type_2 [Hausp47.wt.wt.S8]


title: heterozygous_KO-1 [Hausp48.het.S4]

value: Heterozygous knock-out of USP7 in the hematopoeitic system


title: heterozygous_KO-3 [Hausp63.het.S6]


title: dedifferentiated liposarcoma, patient 5


title: AH1263_34_A

description: total RNA, rRNA-depleted


title: miRNA_E50_Nasal_3

city: Davis

first: Sergi

last: Simo

state: CA

address: One Shields Avenue, 3402 Tupper Hall

department: Cell Biology and Human Anatomy

institute: University of California Davis

description:
Sp_6
miRNAseq_Retina_E50_Temporal_vs_Nasal_TPM.xlsx
miRNA_E50_Nasal_3

data_processing:
Base-calling software HCS 1.5/RTA 1.13
The fastq files were processed with expHTS (see https://dl.acm.org/citation.cfm?id=2811442) to remove PCR duplicates, and to trim low quality sequences and adapter contamination, keeping reads of minimum length 30 bases.
Raw counts per gene were normalized using the cpm command in edgeR
Raw counts per miRNA were normalized using the tpm command in edgeR
Genome_build: reference genome: Mmul_1, annotation reference: Ensembl_75
Supplementary_files_format_and_content: Processed data file format: excel; Content: Counts per milion (CPM) and Transcripts per million (TPM) as indicated.

organism: Macaca mulatta

source_name: embryonic retina

extract_protocol:
Total mRNA was extracted from retina tissue punches using the Total RNA purification Plus Micro kit (Norgen Biotek Corp.)
mRNA libraries were prepared using Illumina TruSeq® Stranded Total RNA (with Ribo-Zero Gold) preparation kit and miRNA libraries were prepared using NEBNEXT library generation kit (New England Biolabs Inc.), according to the manufacturer’s instructions.

value: retina

tag: sample area

value: Nasal


title: mRNA_E150_Nasal_1

description:
mRNAseq_Retina_E-50-90-150_Temporal_vs_Nasal_CPM.xlsx
mRNA_E150_Nasal_1

molecule: polyA RNA


title: miRNA_E50_Temporal_3

description:
Sp_9
miRNAseq_Retina_E50_Temporal_vs_Nasal_TPM.xlsx
miRNA_E50_Temporal_3

value: Temporal


title: miRNA_E50_Nasal_1

description:
Sp_2
miRNAseq_Retina_E50_Temporal_vs_Nasal_TPM.xlsx
miRNA_E50_Nasal_1


title: miRNA_E50_Nasal_2

description:
Sp_10
miRNAseq_Retina_E50_Temporal_vs_Nasal_TPM.xlsx
miRNA_E50_Nasal_2


title: mRNA_E90_Nasal_1

description:
mRNAseq_Retina_E-50-90-150_Temporal_vs_Nasal_CPM.xlsx
mRNA_E90_Nasal_1


title: miRNA_E50_Temporal_1

description:
Sp_5
miRNAseq_Retina_E50_Temporal_vs_Nasal_TPM.xlsx
miRNA_E50_Temporal_1


title: mRNA_E150_Temporal_1

description:
mRNAseq_Retina_E-50-90-150_Temporal_vs_Nasal_CPM.xlsx
mRNA_E150_Temporal_1


title: mRNA_E90_Temporal_1

description:
mRNAseq_Retina_E-50-90-150_Temporal_vs_Nasal_CPM.xlsx
mRNA_E90_Temporal_1


title: mRNA_E50_Nasal_3

description:
Sp_6
mRNAseq_Retina_E-50-90-150_Temporal_vs_Nasal_CPM.xlsx
mRNA_E50_Nasal_3


title: mRNA_E50_Nasal_2

description:
Sp_10
mRNAseq_Retina_E-50-90-150_Temporal_vs_Nasal_CPM.xlsx
mRNA_E50_Nasal_2


title: mRNA_E50_Temporal_2

description:
Sp_1
mRNAseq_Retina_E-50-90-150_Temporal_vs_Nasal_CPM.xlsx
mRNA_E50_Temporal_2


title: mRNA_E50_Temporal_3

description:
Sp_9
mRNAseq_Retina_E-50-90-150_Temporal_vs_Nasal_CPM.xlsx
mRNA_E50_Temporal_3


title: AH1263_37_C

description: total RNA, rRNA-depleted


title: mRNA_E50_Temporal_1

description:
Sp_5
mRNAseq_Retina_E-50-90-150_Temporal_vs_Nasal_CPM.xlsx
mRNA_E50_Temporal_1


title: miRNA_E50_Temporal_2

description:
Sp_1
miRNAseq_Retina_E50_Temporal_vs_Nasal_TPM.xlsx
miRNA_E50_Temporal_2


title: mRNA_E50_Nasal_1

description:
Sp_2
mRNAseq_Retina_E-50-90-150_Temporal_vs_Nasal_CPM.xlsx
mRNA_E50_Nasal_1


title: OSUCCC-LTB AML sample [OSU116P]

type: genomic

city: Columbus

first: Christopher

last: OAKES

state: OH

address: 400 W. 12th Avenue, Wiseman Hall, Suite 455

institute: The Ohio State University

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium methylationEPIC using standard Illumina protocol

scan_protocol: BeadArray fluorescence was measured using the Illumina iScan

data_processing:
Data were normalized by the beta mixture quantile (BMIQ) method using the RnBeads analysis software package.
matrix processed value definition: BMIQ normalized Average Beta
matrix signal intensities value definition: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Bone marrow

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated using column-based preparation (Qiagen)

tag: disease state

value: Diagnosis

value: Bone marrow


title: OSUCCC-LTB AML sample [OSU141R]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank

value: Relapse


title: OSUCCC-LTB AML sample [OSU42P]


title: OSUCCC-LTB AML sample [OS54P]


title: OSUCCC-LTB AML sample [OSU34R]


title: OSUCCC-LTB AML sample [OSU116R]


title: OSUCCC-LTB AML sample [OSU141P]


title: OSUCCC-LTB AML sample [OSU33P]


title: OSUCCC-LTB AML sample [OSU40P]


title: OSUCCC-LTB AML sample [OSU54R]


title: OSUCCC-LTB AML sample [OSU33R]


title: OSUCCC-LTB AML sample [OSU40R]


title: OSUCCC-LTB AML sample [OSU58R]


title: Beat AML project [15-00383]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00383]

data_processing:
Data were normalized by the beta mixture quantile (BMIQ) method using the RnBeads analysis software package.
Beta_values.csv.gz: BMIQ normalized Average Beta
Signal_Intensities.csv.gz: Unmethylated and methylated signal intensities


title: Beat AML project [10-00692]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [10-00692]


title: Beat AML project [14-00423]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00423]


title: Beat AML project [16-01237]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01237]


title: Beat AML project [16-01109]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01109]


title: OSUCCC-LTB AML sample [OSU42R]


title: Beat AML project [15-00742]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00742]


title: Beat AML project [17-00033]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [17-00033]


title: Beat AML project [16-01219]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01219]


title: OSUCCC-LTB AML sample [OSU58P]


title: OSUCCC-LTB AML sample [OSU34P]


title: Beat AML project [16-00466]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00466]


title: Beat AML project [15-00175]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00175]


title: Beat AML project [15-00123]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00123]


title: Beat AML project [13-00655]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00655]


title: Beat AML project [16-01216]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01216]


title: Spleen delta Nef 003

city: Pittsburgh

first: SHIVKUMAR

middle: of

last: BIRADAR

state: PA

address: 130 De Soto St

department: Infectious Diseases and Microbiology

institute: University of Pittsburgh

hyb_protocol: Total RNA (50ng) was hybridized to reporter and capture probe sets at 65°C for 24 h. Hybridized samples were loaded on the nCounter Human Immunology v2 Panel.

scan_protocol: Post-hybridization steps and scanning was performed on the nCounter Profiler

data_processing: RCC files were analyzed using nSolver analysis software (Version 4.0) as per the manufacturer's protocols.

label: biotin

source_name: Spleen

label_protocol: Total RNA (50ng) isolated from spleen tissue of BLTS mice was labelled with probes of nCounter Human Immunology v2 Panel

extract_protocol: HIV infected, and PBS-inoculated humanized mice were sacrificed at 5-7 weeks post HIV infection. Fully developed spleen tissue of humanized mice were collected, and single cells were isolated following mechanical dissociation and total RNA was isolated using Qiagen RNA isolation kit Cat# 74104.

treatment_protocol: BLTS humanized mice were divided into four groups of three mice per group and infected with 10ng HIV-p24 or PBS. Three different HIV strains were used. (HIV-WT/ HIV dNef/ HIV-Y115D).

tag: infection

value: HIV dNef


title: Beat AML project [17-00064]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [17-00064]


title: Beat AML project [15-00608]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00608]


title: Beat AML project [12-00066]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [12-00066]


title: Beat AML project [15-00171]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00171]


title: Beat AML project [15-00614]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00614]


title: Beat AML project [16-01102]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01102]


title: Beat AML project [12-00423]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [12-00423]


title: Beat AML project [13-00487]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00487]


title: Beat AML project [13-00497]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00497]


title: Beat AML project [16-01093]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01093]


title: Beat AML project [15-00300]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00300]


title: Beat AML project [13-00658]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00658]


title: Beat AML project [15-00167]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00167]


title: Beat AML project [14-00739]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00739]


title: Beat AML project [14-00781]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00781]


title: Beat AML project [15-00075]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00075]


title: Beat AML project [14-00901]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00901]


title: Beat AML project [14-00798]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00798]


title: Beat AML project [14-00787]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00787]


title: Beat AML project [14-00712]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00712]


title: Beat AML project [14-00359]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00359]


title: Beat AML project [14-00832]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00832]


title: Beat AML project [14-00581]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00581]


title: Beat AML project [14-00329]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00329]


title: Beat AML project [14-00447]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00447]


title: Beat AML project [13-00165]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00165]


title: Beat AML project [14-00023]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00023]


title: Beat AML project [17-00093]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [17-00093]


title: Beat AML project [12-00211]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [12-00211]


title: Beat AML project [16-01254]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01254]


title: Beat AML project [13-00266]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00266]


title: Beat AML project [15-00975]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00975]


title: Beat AML project [16-01151]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01151]


title: Beat AML project [16-01185]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01185]


title: Beat AML project [15-00615]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00615]


title: Beat AML project [13-00615]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00615]


title: Beat AML project [15-00650]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00650]


title: Beat AML project [12-00023]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [12-00023]


title: Beat AML project [16-00524]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00524]


title: Beat AML project [15-00858]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00858]


title: Beat AML project [14-00546]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00546]


title: Beat AML project [16-01225]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01225]


title: Beat AML project [14-00448]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00448]


title: Beat AML project [15-00633]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00633]


title: Beat AML project [13-00500]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00500]


title: Beat AML project [15-00610]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00610]


title: Beat AML project [13-00186]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00186]


title: Beat AML project [13-00425]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00425]


title: Beat AML project [16-00115]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00115]


title: Beat AML project [16-01055]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01055]


title: well differentiated liposarcoma, patient  16

description: gene expression data from retroperitoneal liposarcoma patient

value: well differentiated liposarcoma


title: Beat AML project [11-00090]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [11-00090]


title: Beat AML project [15-00786]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00786]


title: Beat AML project [16-01262]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01262]


title: Beat AML project [15-00045]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00045]


title: Beat AML project [15-00766]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00766]


title: Beat AML project [15-00302]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00302]


title: Beat AML project [16-00547]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00547]


title: Beat AML project [15-00051]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00051]


title: Beat AML project [16-00392]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00392]


title: Beat AML project [14-00658]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00658]


title: Beat AML project [12-00294]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [12-00294]


title: Beat AML project [14-00670]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00670]


title: Beat AML project [15-00148]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00148]


title: Beat AML project [12-00069]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [12-00069]


title: Beat AML project [14-00831]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00831]


title: Beat AML project [15-00717]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00717]


title: Beat AML project [13-00157]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00157]


title: DNA methylation from glioblastoma stem cell GSC11 rep2

city: Clermont-Ferrand

first: franck

last: court

address: 28 Place Henri Dunant

country: France

institute: GReD CNRS

hyb_protocol: Hybridisation on the arrays was performed by Integragen, SA following the Illumina Infinium HD methylation protocol.

scan_protocol: Standard protocol defined by Illumina for EPIC BeadChip

data_processing:
GenomeStudio V2011.1
The 'Matrix signal intensities.txt' contains Unmethylated and methylated signal intensities

label_protocol: Bisulfite conversion was performed by Integragen, SA.

growth_protocol: Glioblastoma stem cells were cultured in Neurobasal Medium supplemented with B27 1%; N2 0.5%; bFGF 0.05% and EGF 0.005% at 37°C in 5% CO2 humidified incubator. Culture medium was replaced twice a week and when spheres became large and numerous, they were enzymatically dissociated with accutase. Glioblastoma stem cell cultures were characterized by assessing self renewal, differentiation and tumorigenic ability as well as their expression of stemness markers (CD133, SOX2). Finally, all cultures were also classified according to Verhaak's classification of glioblastomas using the method of classification to nearest centroids (ClaNC) with a 840 gene signature.

extract_protocol: DNA was isolated from frozen cells using the QIAamp DNA Mini Kit (Qiagen), according to the manufacturer’s recommendations

treatment_protocol: SMART vector non targeting PGK-TurboGFP (VSC11713) was purchased from GE Healthcare (Little Chalfont, UK). Viral particles were produced and concentrated by the Vectorology platform of Montpellier (Biocampus, Montpellier, France). GSCs were infected using a multiplicity of infection of 10 and were snap frozen 120 h later

tag: cell line

value: Glioblastoma stem cells

value: non targeting shRNA


title: Beat AML project [16-00731]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00731]


title: DNA methylation from glioblastoma stem cell GSC11 rep1


title: Beat AML project [16-00351]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00351]


title: Beat AML project [13-00226]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00226]


title: Beat AML project [16-00220]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00220]


title: Beat AML project [16-00595]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00595]


title: Beat AML project [16-00056]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00056]


title: Beat AML project [13-00365]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00365]


title: Beat AML project [15-00702]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00702]


title: Beat AML project [14-00021]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00021]


title: Beat AML project [15-00855]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00855]


title: Beat AML project [16-00278]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00278]


title: Beat AML project [15-00693]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00693]


title: Beat AML project [16-01223]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01223]


title: Beat AML project [16-00880]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00880]


title: Beat AML project [16-00094]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00094]


title: Beat AML project [15-00892]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00892]


title: Beat AML project [15-00813]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00813]


title: Beat AML project [16-00818]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00818]


title: Beat AML project [16-01049]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01049]


title: Beat AML project [16-00699]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00699]


title: Beat AML project [16-00510]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00510]


title: Beat AML project [16-00525]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00525]


title: Beat AML project [16-00867]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00867]


title: Beat AML project [15-00961]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00961]


title: Beat AML project [16-00540]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00540]


title: Beat AML project [14-00477]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00477]


title: Beat AML project [16-00810]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00810]


title: Beat AML project [16-00273]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00273]


title: Beat AML project [16-00109]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00109]


title: Beat AML project [16-00465]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00465]


title: Beat AML project [15-00870]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00870]


title: Beat AML project [13-00028]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00028]


title: Beat AML project [15-00688]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00688]


title: Beat AML project [16-01100]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01100]


title: Beat AML project [16-00269]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00269]


title: Beat AML project [15-00578]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00578]


title: Beat AML project [16-00078]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00078]


title: Beat AML project [13-00396]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00396]


title: Beat AML project [16-01121]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01121]


title: Beat AML project [15-00680]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00680]


title: Beat AML project [15-00756]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00756]


title: Beat AML project [16-00027]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00027]


title: Beat AML project [16-00981]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00981]


title: Beat AML project [16-00498]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00498]


title: Beat AML project [15-00807]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00807]


title: Beat AML project [13-00354]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00354]


title: Beat AML project [14-00125]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00125]


title: Beat AML project [14-00092]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00092]


title: Beat AML project [16-00815]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00815]


title: Beat AML project [17-00094]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [17-00094]


title: Beat AML project [15-00471]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00471]


title: Beat AML project [15-00763]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00763]


title: Beat AML project [16-00836]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00836]


title: Beat AML project [15-00767]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00767]


title: Beat AML project [16-01191]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01191]


title: Beat AML project [13-00513]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00513]


title: Beat AML project [14-00613]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00613]


title: Beat AML project [14-00041]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00041]


title: Beat AML project [16-00007]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00007]


title: Beat AML project [16-00001]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00001]


title: Beat AML project [15-00464]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00464]


title: Beat AML project [13-00255]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00255]


title: Beat AML project [16-00354]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00354]


title: Beat AML project [13-00393]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00393]


title: Beat AML project [14-00543]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00543]


title: Beat AML project [14-00464]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00464]


title: Beat AML project [15-00417]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00417]


title: Beat AML project [15-00296]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00296]


title: Beat AML project [13-00535]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00535]


title: Beat AML project [14-00193]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00193]


title: Beat AML project [14-00240]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00240]


title: Beat AML project [17-00025]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [17-00025]


title: Beat AML project [15-00670]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00670]


title: Beat AML project [16-00344]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00344]


title: Beat AML project [13-00034]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00034]


title: Beat AML project [15-00900]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00900]


title: Beat AML project [15-00269]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00269]


title: Beat AML project [16-00519]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00519]


title: Beat AML project [14-00272]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00272]


title: Beat AML project [15-00338]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00338]


title: Beat AML project [16-00701]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00701]


title: Beat AML project [16-00026]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00026]


title: Beat AML project [16-00067]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00067]


title: Beat AML project [16-00120]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00120]


title: Beat AML project [16-00041]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00041]


title: Beat AML project [14-00231]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00231]


title: Beat AML project [15-00470]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00470]


title: Beat AML project [16-00292]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00292]


title: Beat AML project [16-00035]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00035]


title: Beat AML project [16-00271]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00271]


title: Beat AML project [16-00157]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00157]


title: Beat AML project [15-00990]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00990]


title: Beat AML project [16-00102]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00102]


title: Beat AML project [16-00075]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00075]


title: Beat AML project [14-00559]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00559]


title: Beat AML project [16-00289]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00289]


title: Beat AML project [14-00034]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00034]


title: Beat AML project [14-00817]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00817]


title: Beat AML project [15-00872]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00872]


title: Beat AML project [16-00070]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00070]


title: Beat AML project [15-00965]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00965]


title: Beat AML project [14-00335]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00335]


title: Beat AML project [16-00003]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00003]


title: Beat AML project [16-00145]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00145]


title: Beat AML project [15-00279]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00279]


title: Beat AML project [14-00578]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00578]


title: Beat AML project [14-00141]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00141]


title: Beat AML project [14-00052]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00052]


title: Beat AML project [14-00504]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00504]


title: Beat AML project [14-00434]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00434]


title: Beat AML project [14-00135]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00135]


title: Beat AML project [13-00454]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00454]


title: Beat AML project [14-00259]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00259]


title: Beat AML project [14-00279]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00279]


title: Beat AML project [15-00261]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00261]


title: Beat AML project [14-00567]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00567]


title: Beat AML project [16-00474]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00474]


title: Beat AML project [14-00289]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00289]


title: Beat AML project [14-00126]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00126]


title: Beat AML project [15-00556]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00556]


title: Beat AML project [14-00774]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00774]


title: Beat AML project [15-00734]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00734]


title: Beat AML project [12-00301]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [12-00301]


title: Beat AML project [16-00410]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00410]


title: Beat AML project [14-00514]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00514]


title: Beat AML project [12-00127]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [12-00127]


title: Beat AML project [16-00494]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00494]


title: Beat AML project [13-00146]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00146]


title: Beat AML project [13-00544]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00544]


title: Beat AML project [13-00204]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00204]


title: Beat AML project [13-00245]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00245]


title: Beat AML project [16-01098]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01098]


title: Beat AML project [15-00616]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00616]


title: Beat AML project [13-00163]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00163]


title: Beat AML project [16-01005]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01005]


title: OSUCCC-LTB AML sample [AML27]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML27]


title: Beat AML project [16-00004]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00004]


title: OSUCCC-LTB AML sample [AML26]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML26]


title: OSUCCC-LTB AML sample [AML25]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML25]


title: OSUCCC-LTB AML sample [AML24]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML24]


title: OSUCCC-LTB AML sample [AML22]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML22]


title: OSUCCC-LTB AML sample [AML21]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML21]


title: OSUCCC-LTB AML sample [AML20]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML20]


title: OSUCCC-LTB AML sample [AML19]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML19]


title: OSUCCC-LTB AML sample [AML15]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML15]


title: OSUCCC-LTB AML sample [AML17]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML17]


title: OSUCCC-LTB AML sample [AML13]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML13]


title: OSUCCC-LTB AML sample [AML18]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML18]


title: OSUCCC-LTB AML sample [AML16]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML16]


title: OSUCCC-LTB AML sample [AML14]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML14]


title: Beat AML project [15-00248]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00248]


title: OSUCCC-LTB AML sample [AML12]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML12]


title: OSUCCC-LTB AML sample [AML10]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML10]


title: OSUCCC-LTB AML sample [AML11]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML11]


title: OSUCCC-LTB AML sample [AML9]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML9]


title: OSUCCC-LTB AML sample [AML2]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML2]


title: OSUCCC-LTB AML sample [AML3]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML3]


title: OSUCCC-LTB AML sample [AML5]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML5]


title: OSUCCC-LTB AML sample [AML4]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML4]


title: OSUCCC-LTB AML sample [AML7]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML7]


title: OSUCCC-LTB AML sample [AML8]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML8]


title: OSUCCC-LTB AML sample [AML1]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML1]


title: OSUCCC-LTB AML sample [AML6]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML6]


title: OSUCCC-LTB AML sample [AML41R]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML41R]


title: OSUCCC-LTB AML sample [AML23]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML23]


title: OSUCCC-LTB AML sample [AML42R]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML42R]


title: OSUCCC-LTB AML sample [AML38R]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML38R]


title: OSUCCC-LTB AML sample [AML36R]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML36R]


title: OSUCCC-LTB AML sample [AML37R]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML37R]


title: OSUCCC-LTB AML sample [AML34R]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML34R]


title: OSUCCC-LTB AML sample [AML35R]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML35R]


title: OSUCCC-LTB AML sample [AML33R]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML33R]


title: OSUCCC-LTB AML sample [AML32R]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML32R]


title: OSUCCC-LTB AML sample [AML31R]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML31R]


title: OSUCCC-LTB AML sample [AML29R]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML29R]


title: Beat AML project [17-00963]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [17-00963]


title: OSUCCC-LTB AML sample [AML28R]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML28R]


title: Beat AML project [17-00350]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [17-00350]


title: Beat AML project [16-01118]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01118]


title: Beat AML project [16-01097]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01097]


title: Beat AML project [16-01094]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01094]


title: OSUCCC-LTB AML sample [AML43R]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML43R]


title: Beat AML project [14-00639]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00639]


title: Beat AML project [10-00542]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [10-00542]


title: OSUCCC-LTB AML sample [AML43P]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML43P]


title: OSUCCC-LTB AML sample [AML40R]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML40R]


title: Beat AML project [16-00684]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00684]


title: Beat AML project [14-00015]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00015]


title: Beat AML project [15-00482]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00482]


title: Beat AML project [10-00792]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [10-00792]


title: Beat AML project [11-00295]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [11-00295]


title: OSUCCC-LTB AML sample [AML39R]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML39R]


title: OSUCCC-LTB AML sample [AML41P]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML41P]


title: OSUCCC-LTB AML sample [AML39P]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML39P]


title: OSUCCC-LTB AML sample [AML40P]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML40P]


title: OSUCCC-LTB AML sample [AML38P]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML38P]


title: OSUCCC-LTB AML sample [AML36P]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML36P]


title: OSUCCC-LTB AML sample [AML34P]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML34P]


title: Aged_5

city: Brisbane

first: Christian

last: Nefzger

state: Queensland

address: 306 Carmody Road

department: Institute for Molecular Biology

country: Australia

institute: The University of Queensland

data_processing:
Sample reads were aligned to the mouse genome (GENCODE GRCm38 primary assembly) using STAR version 2.4.2a ( --outFilterMatchNminOverLread 0.3 --outFilterScoreMinOverLread 0.3)
Reads with duplicated UMIs were removed using the software Je option markdupes
Transcript quantification was performed using feature Counts (exonic regions of GENCODE’s vM15 annotation version)75, and transcripts with more than 5 sequencing reads and 2 count per million of mapped reads in at least two sample were used for further analysis. This resulted in a filtered count matrix of 16154 genes.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample (*.txt) format

source_name: Hematopoietic Stem Cells (HSC)

extract_protocol:
RNA was extracted and purified from young and aged HSC (20,000-25,000 cells from individual mice) using Direct-zol RNA micro kit (Zymo Resarch) according to the manufacturer's instructions (RNA integrity number value >8)
3-prime biased approach was used to generate sequencing libraries. An 8bp sample index anda. 10bp unique molecular identifiery (UMI) were added during the initial poly(A) priming and pooled samples were amplified using a template swithcing oligonucleotide.  The Illumina P5 (5' AAT GAT ACG GCG ACC ACC GA 3') and P7 (5' CAA GCA GAA GAC GGC ATA CGA GAT 3') sequences were added by PCR and Nextera transposase, respectively. The library was designed so that the forward read (R1) utilizes a custom primer (5' GCC TGT CCG CGG AAG CAG TGG TAT CAA CGC AGA GTA C 3') to sequence directly into the index and then the 10 bp UMI. The reverse read (R2) uses the standard R2 primer to sequence the cDNA in the sense direction for transcript identification.

value: Hematopoietic Stem Cells (HSC)

tag: treatment nr

value: Aged (20-24 months)

tag: gender

value: female


title: OSUCCC-LTB AML sample [AML33P]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML33P]

tag: tissue


title: Aged+NR_3

tag: cell type

value: Nicotamide Riboside

tag: age


title: Aged+NR_4


title: OSUCCC-LTB AML sample [AML32P]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML32P]


title: OSUCCC-LTB AML sample [AML31P]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML31P]


title: OSUCCC-LTB AML sample [AML42P]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML42P]


title: OSUCCC-LTB AML sample [AML29P]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML29P]


title: Aged_2


title: Beat AML project [16-01022]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01022]


title: Aged_3


title: OSUCCC-LTB AML sample [AML28P]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML28P]


title: Young_5

value: Young (6-12 weeks)


title: Aged_1


title: Young_4


title: Aged+NR_5


title: Beat AML project [16-00303]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-00303]


title: Beat AML project [16-01138]

description:
Relapse bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [16-01138]


title: Young_3


title: OSUCCC-LTB AML sample [AML37P]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML37P]


title: Beat AML project [15-00778]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00778]


title: Young_2


title: OSUCCC-LTB AML sample [AML35P]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from The Ohio State Comprehensive Cancer Center Leukemia Tissue Bank [AML35P]


title: Aged+NR_2


title: Beat AML project [15-00563]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00563]


title: Aged+NR_1


title: Young_1


title: Beat AML project [15-00377]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00377]


title: Aged_4


title: Beat AML project [15-00276]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00276]


title: Rif1-KO3

city: Basel

first: Ilya

middle: M.

last: Flyamer

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description:
KO_28-2
Rif1-KO.mm10.mapq_30.1000.mcool

data_processing:
FASTQ files were processed with the distiller pipeline (https://github.com/mirnylab/distiller-nf, DOI:10.5281/zenodo.2630563) to obtain .mcool files used in downstream analyses.
Briefly, reads were mapped to the mm19 genome assembly, Hi-C valid pairs were identified using pairtools, and they were used for construction of .cool files a1000 bp resolution.They were then zoomified to obtain .mcool failes with multiple resolutions, and each resolution was balanced.
Genome_build: mm10
Supplementary_files_format_and_content: .mcool files with binned Hi-C data (https://cooler.readthedocs.io/en/latest/)

source_name: mESCs

growth_protocol: Mouse embryonic stem cell (ESC) cells were derived as described in (Foti, Gnan et al. 2016), with the addition of 1 μM MEK inhibitor PD0325901 and 3 μM GSK3 inhibitor CHIR99021 (MRC PPU Reagents and Services, School of Life Sciences, The University of Dundee) in the culture media, from the start of the protocol.  ESCs were grown at 37°C in 7.5 % CO2 in Knockout DMEM (Gibco 10829-018), containing 12.5% heat-inactivated fetal bovine serum (Pan-Biotech), 1 % non-essential amino acids (Gibco 11140-035), 1% Penicillin/Streptomycin (Gibco 15070063), 0.1 mM 2-Mercaptoethanol (Gibco 31350-010), 1% L-Glutamine (Gibco 25030024)), supplemented with 1 μM PD0325901 and 3 μM CHIR99021 and 20 ng/ml leukemia inhibitory factor (LIF, EMBL Protein Expression and Purification core facility).

extract_protocol:
After four days of OHT treatment, cells were collected and counted. Cells were washed twice in cold DPBS and resuspended in full media. Samples were crosslinked for 10 minutes rotating at room temperature in 1% formaldehyde (106 cells/ml). Crosslinking was stopped by adding glycine at the final concentration of 0.2 M for 5 minutes at RT. Samples were washed twice in cold DPBS and pellets were snap frozen. 2-5 × 106 cells per sample were lysed in 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% IGEPAL (Sigma, I3021) supplemented with protease inhibitor (Thermo Scientific, 78430) for 15 minutes on ice. Nuclei were washed twice in cold lysis buffer, resuspended in 50 μl of NEBuffer 3.1 (NEB, B7003S) supplemented with 0.3% SDS and incubated at 62°C for 10 minutes. After diluting and quenching the SDS by adding 57.5 μl of NEBuffer 3 and 12.5 μl of 20% Triton X-100 (Sigma, 93443), samples were incubated at 37°C for 60 minutes. Nuclei were spun and incubated in 250 μl of 1× DpnII buffer with 600 U of DpnII restriction enzyme (NEB, R0543L) overnight at 37°C. An additional 200 U of DpnII were added to each sample the following day and incubated for a further 2 hours.  After heat inactivation of DpnII for 20 min at 65°C, restriction fragments ends were filled by DNA polymerase I, Large (Klenow) Fragment (NEB, M0210), 0.8 U/μl of DNA, in 50 μl of 0.3 mM biotin-14-dATP (Thermo Fisher, 19524016), 0.3 mM dCTP/ dGTP/ dTTP for 1.5 hours at 37°C.  900 μl of ligation master mix were then add to the samples: 1.33x NEB T4 DNA ligase buffer (NEB, B0202), 1.1% Triton X-100, 1.33 mg of Bovine Serum Albumin and 2000 U of T4 DNA Ligase (NEB, M0202). Samples were incubated for 4 hours rotating. Nuclei were spun and resuspended in water and digested with proteinase K (Sigma, P6556) 1.2 mg/ml and 0.8% SDS at 55°C for 30 minutes. 130 μl of 5 M NaCl were added and samples were incubated at 65°C overnight.
After ethanol precipitation, DNA was resuspended in 500 μl of 10 mM Tris-HCl pH8.0 and washed trice using the same buffer using Amicon filters (Millipore, UFC503096). Samples were diluted in 50 mM Tris pH 8.0, 0.1% SDS, 10 mM EDTA and sonicated to about 500 bp using a probe-based sonicator. Washes were then repeated as in the previous step. Biotinylated DNA was pulled down using 30 ul of 10 mg/ml Dynabeads MyOne Streptavidin T1 beads (Life technologies, 65602) in 10 mM Tris-HCl (pH 7.5); 1 mM EDTA; 2 M NaCl for 15 minutes at room temperature rotating. Beads were washed in TWB: 5 mM Tris-HCl (pH 7.5); 0.5 mM EDTA; 1 M NaCl; 0.05% Tween 20 for 2 minutes at 55° C twice, resuspended in 20 ul 1× NEB T4 DNA ligase buffer, transferred to a new tube and incubated for 30 minutes at room temperature with 100 μl of: 1x NEB T4 DNA ligase buffer, 0.5 mM dNTPs, 50 U T4 PNK (NEB, M0201), 12 U T4 DNA polymerase I (NEB, M0203), 5 U DNA polymerase I, Large (Klenow) Fragment. After two washes in TWB at 55°C for 2 minutes, beads were transferred to 1× NEBuffer 2 (NEB, B7002S) and moved to a new tube. Beads were then incubated at 37°C for 30 minutes in 100 ul of 0.9X NEBuffer 2, 0.5 mM dATP and 25 U Klenow exo minus (NEB, M0212). Beads were washed again as before and transferred to T4 ligation buffer. DNA was ligated for 2.5 hours with Illumina adaptors in 50 μl of the following reaction mix: 1X T4 ligation buffer, 1.2 µM Illumina adaptors, 1U T4 DNA ligase. Beads were washed once again with TWB as before, to be then resuspended and stored in 50 μl of 10 mM Tris-HCl (pH8.0).  Libraries were amplified in six parallel 50 µl PCR reactions using Illumina primers and 4 μl of beads (or DNA removed off the beads by heating at 95°C for 20 min) per reaction after testing optimal amplification cycles. Size selection was performed on an agarose gel, isolating fragments between 300-700 base pairs, followed by purification with QIAquick Gel Extraction Kit (Qiagen 28704).
Each library was test sequenced at low depth to test its quality, and then selected libraries were sequenced on the equivalent of approximately one mid-output lane of Illumina NextSeq 500/550 (75 bp  paired end reads). All data were used in the final analyses.

treatment_protocol: Experiments were carried out each time from a frozen vial of cells, at least two passages after thawing. 5.2x10e6 cells for Rif1-WT and 6.5x10e6 Rif1-KO lines, per 15 cm plate (or the equivalent for different sized plates) were plated at day zero, when treatment with 200 nM 4-hydroxytamoxifen (OHT, Sigma H7904) started. Fresh medium with OHT was added after 48 hours. Cells were collected about 96 hours after starting OHT treatment.

tag: genotype

value: ESCs

value: Proximity ligated genomic DNA


title: Rif1-KO2

description:
KO_18
Rif1-KO.mm10.mapq_30.1000.mcool


title: Beat AML project [13-00353]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [13-00353]


title: Beat AML project [10-00669]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [10-00669]


title: Rif1-KO1

description:
KO_24
Rif1-KO.mm10.mapq_30.1000.mcool


title: Rif1-WT3

description:
WT_37.5
Rif1-WT.mm10.mapq_30.1000.mcool


title: Beat AML project [10-00507]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [10-00507]


title: Beat AML project [09-00705]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [09-00705]


title: Rif1-WT2

description:
WT_F
Rif1-WT.mm10.mapq_30.1000.mcool


title: Beat AML project [15-00653]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [15-00653]


title: glioma sample;IDHwt_GIII_38

hyb_protocol: DNA and array processing were performed by the Genomic Platform/ Curie Institute (France) according to the manufacturer's protocol.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Scanned data files were analyzed with Affymetrix Chromosome Analysis Suite v3.1 (ChAS) (Affymetrix Inc., USA) using the CytoScanHD_Array.na33.annot.db annotation file on hg19 genome. To find copy numbers variations, single sample analysis strategy were done using the reference model file “CytoScanHD_Array.na33.r2.REF_MODEL”. To prevent false positive CNVs detection arising due to inherent microarray “noise”, only alterations that involved at least 50 consecutive probes and spanning more than 100 kbp were considered in the analysis.
The file CNV_SSA_Results.txt contains a matrix of CNV fragments from single sample analyses

source_name: DNA from Glioma sample

growth_protocol: Immediately after surgery, glioma samples were snap-frozen and stored in liquid nitrogen. non-tumoral control brain samples were cadaveric specimens removed by autopsy 4-16 h following accidental death (Brain and Tissue Bank of Maryland).

extract_protocol: DNA  were isolated from frozen  tissue samples  using the QIAamp DNA Mini Kit (Qiagen, Hamburg, GmbH)

value: glioma

tag: gliomas classification (grade)

value: Grade IIII

tag: gliomas classification

value: IDH statut:IDHwt


title: healthy donor 3; frontal cortex

source_name: DNA from  frontal cortex

label_protocol: DNA and array processing were performed by the Genomic Platform/ Curie Institute (France) according to the manufacturer's protocol.

value: healthy frontal cortex

value: not applicable

value: IDH statut:not applicable


title: glioma sample;IDHmut_GIII_32

value: IDH statut:IDHmut


title: glioma sample;IDHwt_GIII_27


title: glioma sample;IDHwt_GIII_35


title: glioma sample;IDHwt_GIII_33


title: Beat AML project [14-00228]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [14-00228]

value: Diagnosis

value: Bone marrow


title: glioma sample;IDHwt_GIII_20


title: glioma sample;IDHwt_GIII_18


title: Beat AML project [10-00136]

description:
Diagnosis bone barrow sample
Bone marrow-derived genomic DNA sample obtained from the Beat AML project [10-00136]


title: glioma sample;IDHwt_GIII_10


title: glioma sample;IDHwt_GIII_8


title: glioma sample;IDHwt_GIII_3


title: glioma sample;IDHwt_GIII_2


title: glioma sample;IDHmut_GIII_1


title: glioma sample;IDHmut_GII_14

value: Grade II


title: mBL_68_hybridized to U133 plus 2.0 array

city: Omaha

first: Javeed

last: Iqbal

state: NE

address: 601 S 42nd St

institute: UNMC

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing: Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Affymetrix Genotyping console software. Log2 intensities were generated from genotyping console were exported for further processing using the DNAcopy package for R. For gene expression data profiled by Affymetrix U133 plus 2.0 array, the raw signal intensities were imported into BRB-ArrayTools (v 4.5.0)  and normalized by MAS 5.0 with default settings.

source_name: tumor biopsy

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA and total RNA was extracted from cryopreserved lymphoma tissue using the Qiagen AllPrep DNA/RNA kit. DNA and RNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: tumor type

value: lymphoma

tag: age group

value: Pediatric


title: mBL_74_hybridized to U133 plus 2.0 array

value: Adult


title: mBL_67_hybridized to U133 plus 2.0 array


title: mBL_71_hybridized to U133 plus 2.0 array


title: glioma sample;IDHmut_GII_13


title: mBL_65_hybridized to U133 plus 2.0 array


title: mBL_9_hybridized to U133 plus 2.0 array


title: glioma sample;IDHwt_GIII_26


title: mBL_66_hybridized to U133 plus 2.0 array


title: glioma sample;IDHmut_GII_9


title: mBL_69_hybridized to U133 plus 2.0 array


title: mBL_72_hybridized to U133 plus 2.0 array


title: mBL_64_hybridized to U133 plus 2.0 array


title: glioma sample;IDHmut_GII_7


title: mBL_73_hybridized to U133 plus 2.0 array


title: mBL_63_hybridized to U133 plus 2.0 array


title: mBL_62_hybridized to U133 plus 2.0 array


title: mBL_59_hybridized to U133 plus 2.0 array


title: mBL_61_hybridized to U133 plus 2.0 array


title: mBL_57_hybridized to U133 plus 2.0 array


title: mBL_58_hybridized to U133 plus 2.0 array


title: glioma sample;IDHmut_GII_3


title: mBL_56_hybridized to U133 plus 2.0 array


title: mBL_60_hybridized to U133 plus 2.0 array


title: glioma sample;IDHwt_GBM_35

value: GBM


title: glioma sample;IDHwt_GII_1


title: glioma sample;IDHwt_GBM_32


title: glioma sample;IDHwt_GBM_25


title: mBL_52_hybridized to U133 plus 2.0 array


title: glioma sample;IDHwt_GBM_20


title: glioma sample;IDHwt_GBM_18


title: glioma sample;IDHwt_GBM_19


title: glioma sample;IDHwt_GBM_17


title: mBL_54_hybridized to U133 plus 2.0 array


title: glioma sample;IDHwt_GBM_16


title: mBL_53_hybridized to U133 plus 2.0 array


title: glioma sample;IDHwt_GBM_12


title: glioma sample;IDHwt_GBM_14


title: glioma sample;IDHwt_GBM_22


title: glioma sample;IDHwt_GBM_11


title: glioma sample;IDHwt_GBM_10


title: mBL_49_hybridized to U133 plus 2.0 array


title: mBL_5_hybridized to U133 plus 2.0 array


title: mBL_55_hybridized to U133 plus 2.0 array


title: mBL_50_hybridized to U133 plus 2.0 array


title: mBL_43_hybridized to U133 plus 2.0 array


title: mBL_42_hybridized to U133 plus 2.0 array


title: mBL_48_hybridized to U133 plus 2.0 array


title: mBL_41_hybridized to U133 plus 2.0 array


title: mBL_44_hybridized to U133 plus 2.0 array


title: mBL_51_hybridized to U133 plus 2.0 array


title: glioma sample;IDHwt_GBM_8


title: glioma sample;IDHwt_GBM_15


title: Patient 9

city: Saint-Petersburg

first: Aleksandr

last: Khudiakov

address: 2, Akkuratova

department: Institute of molecular biology and genetics

country: Russia

institute: Almazov National Medical Research Centre

description:
small RNA
sample 9

data_processing:
Obtained paired-end reads were trimmed for adaptor sequences, merged using FLASH tool, length filtered 15-31 bp using Geneious Prime 2020.0.5 and then aligned to the mature microRNA database (miRbase,release 22.1) using Novoalign implemented in mirPRo tool.
Counts were normalized using DESeq2 package.
Genome_build: miRbase, release 22.1
Supplementary_files_format_and_content: Table with normalized miRNA counts for every miRNA and every sample

source_name: Pericardial fluid

extract_protocol:
Before RNA extraction, pericardial fluid samples were double centrifugated at 3000 g at 4°C for 15 min and obtained supernatant was used for RNA extraction. Small RNAs were extracted using SPLIT RNA Extraction Kit (Lexogen) according to manufacturer’s recommendations.
Small RNA libraries were generated using Small RNA-Seq Kit (Lexogen) according to manufacturer’s recommendations. The number of amplification cycles was 20 for all samples.

value: Pericardial fluid

tag: disease

value: arrhythmogenic right ventricular cardiomyopathy


title: Patient 8

description:
small RNA
sample 8


title: Acute myeloid leukemia cell line UCSD-AML1

city: Freiburg

first: Gabriele

last: Greve

address: Hugstetter Str 55

department: Department of Internal Medicine 1

institute: University of Freiburg Medical Center

hyb_protocol: according to manufacturer (Affymetrix)

scan_protocol: according to manufacturer (Affymetrix)

data_processing: CEL files were analysed using the Affymetrix Chromosome Analysis Suite ChAS (USCD-AMl1/ELF-153/KG-1) and the Affymetrix Genoyping Console Software (U937); data was annotated to the reference genome assembly GRCh37(hg19).

label_protocol: Samples were labeled using the Affymetrix CytoScan Reagent and the SNP 6.0 Core Reagent Kits (USCD-AML1/ELF-153/KG-1 and U937, respectively)

growth_protocol: KG-1 and U937 were grown in RPMI supplemented with 10 % fetal calf serum and 1 % penicillin/streptomycin. UCSD-AML1 and ELF-153 were grown in RPMI supplemented with 20 % fetal calf serum, 1 % penicillin/streptomycin and 5 ng/ml human GM-CSF.

extract_protocol: Genomic DNA was extracted using the Quiagen DNeasy Blood and Tissue DNA extraction Kit according to manufacturer's protocol.

treatment_protocol: All cell lines were untreated prior to SNP analysis.

value: Acute myeloid leukemia cell line


title: Acute myeloid leukemia cell line KG-1

source_name: Acute myeloid leukemia cell line KG-1


title: Acute myeloid leukemia cell line ELF-153


title: mBL_36_hybridized to U133 plus 2.0 array


title: mBL_40_hybridized to U133 plus 2.0 array


title: Patient 7

description:
small RNA
sample 7


title: glioma sample;IDHwt_GBM_6

value: glioma


title: mBL_37_hybridized to U133 plus 2.0 array


title: mBL_39_hybridized to U133 plus 2.0 array


title: mBL_38_hybridized to U133 plus 2.0 array


title: mBL_35_hybridized to U133 plus 2.0 array


title: Patient 5

description:
small RNA
sample 5


title: mBL_33_hybridized to U133 plus 2.0 array


title: mBL_34_hybridized to U133 plus 2.0 array


title: mBL_31_hybridized to U133 plus 2.0 array


title: mBL_30_hybridized to U133 plus 2.0 array


title: Patient 4

description:
small RNA
sample 4


title: Patient 3

description:
small RNA
sample 3

value: coronary artery disease, post-infarction ventricular tachycardia


title: mBL_32_hybridized to U133 plus 2.0 array


title: mBL_29_hybridized to U133 plus 2.0 array


title: mBL_28_hybridized to U133 plus 2.0 array


title: Patient 2

description:
small RNA
sample 2


title: mBL_27_hybridized to U133 plus 2.0 array


title: Patient 1

description:
small RNA
sample 1


title: Patient 6

description:
small RNA
sample 6


title: control_2008_101d_Yellow_6_GCCAAT_L003

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

description: Grown in loess over glacial outwash, and the soil series was a Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls). The surface horizon contained approximately 110 g sand, 580 g silt, and 310 g clay kg-1. Total nitrogen in the 0-15 and 15-60 cm depths were approximately 5.1 and 10.2 mg N ha-1, respectively. Total C in the 0-15 and 15-60 cm depths were approximately 44.6 and 78.5 mg C ha-1, respectively. Additional information about soil at the site is available in Clay et al. (1994) and Clay et al. (1995). N-rate application of 236 kg/ha (based on SDSU soil test recommendations for a yield goal of 13,000 kg/ha) was applied to all plots, and supplemental water was added as needed based on the checkbook method of irrigation management (Werner 1993) to limit water stress by overhead sprayers. Irrigation was applied in four applications in 2007 and 2008, totaling approximately 10 cm each year.

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 the forward reads were mapped to the Zea Mays Enseble19 refernce genome using the tophat2 SE program in the iPlant (now CyVerse) dicovery environment with default perameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated usung the cuffdiff2 program in the iPlant (now CyVerse) dicovery environment with default perameters.
Genome_build: esnemble 19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Zea mays

source_name: Mature leaf tip

extract_protocol:
leaf tips were cut from the plants and placed in 50 ml plastic tubes. Tubes were filled with liquid N2 and moved to storage at -80C prior to extraction. Tissues were ground in liquid N2 and RNA was extracted using a modified pine tree extraction protocol or were extracted using the trizol extraction procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: planted on May 1, 2007 or May 7, 2008 at a seeding rate of approximately 32,000 seeds ha−1, with row spacing of 76 cm. Plants were either left weed free as a controls or were grown with weeds. To determine weed effects that persist after weed growth during the CWFP, some plots had weeds removed at V4. For 2007 weedy and weed removed (WR) plots, endemic velvetleaf populations consisted of between 34-60 weeds m-1 row, whereas the 2008 weedy and WR plots, canola was drilled 10 cm from the maize row at 7 kg ha−1 at maize planting. Control plots were kept weed free with a pretreatment of Dual II Magnum at 1.5 pts/ac - May 3, 2007 and May 9, 2008 and Roundup WeatherMax at 32 oz/acre - June 18, 2007 and June 14. 2008. For weed removal at V4, WR plots were also treated with Roundup WeatherMax at 32 oz/acre.  Weedy plots were not treated with Roundup prior to harvest. A randomized complete block design was used with four replications.

tag: strain

value: commercially available 97-d maize hybrid that had glyphosate-resistance and maize rootworm/maize borer stacked traits

value: pooled mature leaf tips from at least 4 individual plants

tag: treament

value: control (weed free)

tag: collection date

tag: temperature at tme of collection

tag: collection time


title: control_2008_410d_red7_CAGATC_L001

growth_protocol: Grown in loess over glacial outwash, and the soil series was a Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls). The surface horizon contained approximately 110 g sand, 580 g silt, and 310 g clay kg-1. Total nitrogen in the 0-15 and 15-60 cm depths were approximately 5.1 and 10.2 mg N ha-1, respectively. Total C in the 0-15 and 15-60 cm depths were approximately 44.6 and 78.5 mg C ha-1, respectively. Additional information about soil at the site is available in Clay et al. (1994) and Clay et al. (1995). N-rate application of 236 kg/ha (based on SDSU soil test recommendations for a yield goal of 13,000 kg/ha) was applied to all plots, and supplemental water was added as needed based on the checkbook method of irrigation management (Werner 1993) to limit water stress by overhead sprayers. Irrigation was applied in four applications in 2007 and 2008, totaling approximately 10 cm each year.


title: Weedy_2008_310d2_A005_1

value: weedy through V8


title: Weedy_2008_407d2_A004