title: JK2.8_Clr4_t4_R1

status: Public on Dec 15 2021

city: Berlin

first: Benedikt

last: Siebecker

address: Gustav-Meyer-Allee 25

institute: Technische Universität Berlin

data_processing:
Obtained read data were first quality controlled via FastQC
STAR was used for mapping the reads to the T. thermophilus ATCC 42464 genome (assembly ASM22609v1)
Data normalization and differential gene expression analysis was performed with DEseq2
Differential gene expression was evaluated with Wald test and Benjamini and Hochberg False Discovery Rate (FDR) with a threshold of 0.05
Genome_build: T. thermophilus ATCC 42464 genome (assembly ASM22609v1)
Supplementary_files_format_and_content: raw count values, normalized raw count values, and differential expression analysis results

organism: Thermothelomyces thermophilus

source_name: RNA isolated from whole biomass

growth_protocol: 1*10^9 spores/L were inoculated in bioreactor medium containing 76 mM (NH4)2SO4, 2 mM MgSO4x7H2O, 12 mM KH2PO4, 7.5 mM KCl, 0.27 mM CaCl2x2H2O, 0.025 mM biotin, 55.5 mM glucose and trace elements (134 µM EDTA disodium salt dihydrate, 70 µM ZnSO4x7H2O, 162 µM H3BO3, 23 µM MnSO4xH2O, 16.4 µM FeSO4x7H2O, 6.5 µM CoCl2x6H2O, 5.8 µM CuSO4x5H2O, 5.7 µM Na2MoO4x2H2O; pH adjusted to 6 using 1 M NaOH). CaCl2x2H2O, glucose and trace elements were autoclaved separately and added to the medium after autoclaving. Biotin was sterile filtrated and added to the medium after autoclaving. Prior to autoclaving pH was set to 6.7 using 10 M NaOH. Prior to inoculation, the temperature was set to 45 °C, pH value to 6.7 (if necessary), stirring to 100 rpm, and aeration to 0.01 slpm (after reaching 100 % DOT). pH regulation was achieved via 25 % ammonia solution and 20 % phosphoric acid. After inoculation, a time-based profile for aeration and stirring was started. Aeration and stirring were constantly increased within 10 h to 1 slpm and 750 rpm, respectively. At the end of the exponential phase when glucose concentration was close to 0-1 g/L (~13 g base addition) chemostat cultivation was started by addition of medium at a dilution rate of 0.1 1/h and maintaining culture broth weight at 5 kg. To prevent foaming, PPG 2000 was added with a rate of 20 mg/h during chemostat cultivation. In steady state, the carbon source was changed to cellulose (autoclaved separately) by removing 500 g culture broth and subsequently adding 450 g bioreactor medium (without glucose) and 50 g microcrystalline cellulose resulting in 5 kg total weight of the culture broth. Cultivation was continued as a batch cultivation.

extract_protocol:
The biomass sample was gained by filtrating the culture broth sample via vacuum filtration, collecting mycelium on a filter. This filter was wrapped in tinfoil and immediately frozen in liquid nitrogen. RNA was isolated with the Trizol reagent (Invitrogen) using frozen ground mycelium according to the manufacturer's instructions. Samples were purified using the innuPREP RNA Mini Kit 2.0 (Analytik Jena) according to the manufacturer's instructions. Possible remaining DNA was removed via DNA-free™ DNA Removal Kit (Invitrogen) according to the manufacturer's instructions. After purification and DNAse treatment, samples were ready for RNA sequencing.   RNA was sequenced at Microsynth AG (Balgach) for strains MJK20.3 and BS6.4 and at GenomeScan (Leiden) for strains BS7.8 and JK2.8 using an Illumina platform with 150 bp reads paired end, polyA enrichment, and > 5 million reads per sample. A quality check of the RNA samples prior to sequencing was included according to the guidelines of the company. Prior to RNA sequencing at GenomeScan (Leiden), no purification and DNAse treatment was performed.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Samples for RNA extraction were taken in exponential state (ex), steady state (SS) and after (t1=0.5 h, t2=1 h, t3=2 h, t4=4 h) the addition of the medium containing cellulose.

value: JK2.8 ([delta]ku80,[delta]clr4)

value: t4= 4 h after spiking cellulose in steady state

tag: replicate

value: replicate 1


title: JK2.8_Clr4_t4_R2_flowcell1

type: SRA

country: Germany

description: read1 flowcell1

library_source: transcriptomic

molecule: polyA RNA

tag: strain

tag: condition

value: replicate 2


title: JK2.8_Clr4_t3_R2

value: t3= 2 h after spiking cellulose in steady state


title: JK2.8_Clr4_t3_R1


title: JK2.8_Clr4_t4_R2_flowcell2

description: read1 flowcell2


title: JK2.8_Clr4_SS_R2

value: steady state-glucose


title: ESCA.P20190404

status: Public on Dec 16 2021

city: Beijing

first: Shishang

last: Qin

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Peking university

description:
processed data file:
ESCA_10X.CD4.counts.txt.gz
ESCA_10X.CD8.counts.txt.gz
metadata.txt.gz
10X_VDJ.merge.txt.gz
bulk_RNA.counts.txt.gz
bulk_Exome.mutation.txt.gz

data_processing:
For 10X data, Cell Ranger 3.0.0 was used to quantify gene expression level and to identify TCR sequences.
For Smart-seq2 data, HTSeqGenie pipeline (R package version 4.8) was used to quantify gene expression level.
For bulk RNAseq data, UCSC Xena Toil RNAseq pipeline was used to quantify gene expression level.
For bulk exome data, BWA-MEM algorithm was used to align the reads to genome, PICARD was used to sorted and de-duplicated the bam files, GATK 3.7 was used to realign reads around INDEL region and re-calibrate base quality, and finally strelka 1.0.14 was used to call somatic mutations (SNV and INDEL).
Genome_build: GRCh38 for RNA expression and TCR data, and b37 for DNA mutation calling.
Supplementary_files_format_and_content: text files for expression matrices, cell metadata, TCR summary, and mutation summary.

organism: Homo sapiens

source_name: ESCA

extract_protocol:
Tumors and adjacent normal tissues were cut into approximately 1-2 mm3 pieces in the RPMI-1640 medium (Gibco) with 10% fetal bovine serum (FBS, Gibco), and enzymatically digested with gentleMACS (Miltenyi) for 60 min on a rotor at 37°C, according to manufacturer’s instruction. The dissociated cells were subsequently passed through a 100 µm SmartStrainer and centrifuged at 400 g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (TIANDZ) and incubated on ice for 1-2 min to lyse red blood cells. After washing twice with 1× PBS (Gibco), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 1% FBS).
Single cell suspensions were stained with antibodies against CD45 and 7AAD for FACS sorting, performed on a BD Aria SORP instrument. Based on FACS analysis, single cells were sorted into 1.5 ml tubes (Eppendorf) and counted manually under the microscope. The concentration of single cell suspensions was adjusted to 500-1200 cells/ul. Cells were loaded between 7,000 and 15,000 cells/chip position using the 10x Chromium Single cell 5’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics, V3 barcoding chemistry) according to the manufacturer’s instructions. All the subsequent steps were performed following the standard manufacturer’s protocols. Purified libraries were analyzed by an Illumina Hiseq X Ten sequencer with 150-bp paired-end reads.
10x Chromium Single cell 5’ + VDJ Library, and Smart-seq2 Library (only for one CHOL sample)

tag: tissue

value: Tumor, Adjacent-normal

tag: platform


title: Capture Sequencing of 134kb SynHoxA assemblon delivered to Hoxa -/- mESC

city: Seattle

first: Sudarshan

last: Pinglay

state: WA

address: 3720 15th Ave NE

country: USA

institute: University of Washington

library_source: genomic

data_processing:
Library strategy: DNA-seq
Illumina adapter trimming with trimmomatic v0.39
Reads mapped using bowtie2 v2.2.9
Sort bam files using samtools
Make bigwig files using deeptools bamCoverage v3.2.1
Genome_build: mm10_synHoxA custom genome or mm10_synHoxA_delHoxA custom genome, mm10 or rn6
Supplementary_files_format_and_content: bigwig files to normalize coverage

molecule: genomic DNA

organism:
Mus musculus
Rattus norvegicus

source_name: Mouse ES cells with variant synthetic Hox clusters

growth_protocol: Plasmids were purified from bacterial cultures in Luria Broth (LB) supplemented with the appropriate antibiotic (12.5 µg/mL Chloramphenicol for source BACs, and 25 µg/mL Kanamycin for all assemblons. mESCs were cultured on plastic tissue culture plates coated with 0.1% gelatin (EMD Millipore ES-006-B) at 37°C and 5% CO2 in ‘80/20’ medium comprising 80% 2i medium and 20% mESC medium. mESCs were grown at 37°C and 8% CO2 before differentiation experiments.  2i medium was made from a 1:1 mix of Advanced DMEM/F12 (Gibco 12634010) and Neurobasal-A (Gibco 10888022), containing 1X N-2 supplement (Gibco 17502048), 1X B-27 supplement (Gibco 17504044), 2mM Glutamax (Gibco 35050061), 0.1mM Beta-Mercaptoethanol (Gibco 31350010), 103 units/mL LIF (Millipore, ESG1107), 1 μM MEK1/2 inhibitor (Stemgent, PD0325901), and 3 μM GSK3 inhibitor (R&D Systems, CHIR99021). mESC medium was made from Knockout DMEM (Gibco 10829018), containing 15% Fetal Bovine Serum (Gemini), 0.1 mM Beta-Mercaptoethanol (Gibco 31350010), 1X MEM Non Essential Amino Acids (Gibco 11140050), Glutamax (Gibco 35050061), 1X Nucleosides (Millipore ES-008-D) and LIF (Millipore ESG1107).

extract_protocol:
Plasmids were purified from small scale bacterial cultures (5-10 mL) using alkaline lysis. gDNA was extracted from mESC cell pellets using Qiagen DNA mini kit.
Illumina sequencing libraries for BACs were generated from 100-200 ng BAC DNA using NEBNext Ultra II FS DNA Library Prep Kit (New England Biolabs E7805S) according to the manufacturer’s protocol. Whole genome sequencing and capture sequencing libraries were prepared as follows: 1 µg of DNA was sheared to ∼500 to 900 bp in a 96-well microplate using the Covaris LE220 (450 W, 10% Duty Factor, 200 cycles per burst, and 90-s treatment time). Sheared DNA was purified using the DNA Clean and Concentrate-5 Kit (Zymo Research D4013), and the concentration was measured on a NanoDrop instrument (Invitrogen). DNA fragments were end-repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase (New England Biolabs M0203S, M0210S and M0201S, respectively), and A-tailed using Klenow (3′-5′ exo-; New England Biolabs M0212L). Illumina-compatible adapters were subsequently ligated to DNA ends, and DNA libraries were amplified with KAPA 2X Hi-Fi Hotstart Readymix (Roche). Biotinylated baits for capture sequencing were prepared from assemblon BACs using nick translation

value: 134kb SynHoxA assemblon in HoxA -/- mESCs

tag: capture bait

value: 134kb SynHoxA BAC

tag: cell type

value: mESC


title: JK2.8_Clr4_t2_R2

value: t2= 1 h after spiking cellulose in steady state


title: JK2.8_Clr4_t2_R1


title: JK2.8_Clr4_t1_R2

value: t1= 0.5 h after spiking cellulose in steady state


title: JK2.8_Clr4_SS_R1


title: JK2.8_Clr4_ex_R2

value: exponential state-glucose


title: JK2.8_Clr4_ex_R1


title: BS7.8_Clr1_t4_R1

value: BS7.8 ([delta]ku80,[delta]clr1)


title: BS7.8_Clr1_t4_R2


title: B1a Control rep2

city: Pohang-Si

first: Hyebeen

last: Hong

address: Cheongam-Ro, 77

department: Department of Life Science

country: South Korea

institute: POSTECH

description:
Spleen
Table_S1.xlsx

data_processing:
1) Quality control analysis of the raw sequenced reads was performed to examine overall reads' quality, total bases, total reads, and GC (%).
2) Artifacts such as low quality reads, adaptor sequences, contaminant DNAs, or PCR duplicates were removed to reduce biases.
3) Trimmed reads were mapped to mouse reference genome with HISAT2, a splice-aware aligner.
4) Transcripts were assembled with aligned reads by StringTie. It provides information of known transcripts, novel transcripts, and alternatively spliced transcripts.
5) Expression profiles were represented as read counts and normalization values, based on the transcript length and depth of coverage. The FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) value was used as a normalization value.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: The differentially expressed genes (DEGs) in Cic-null B-1a and Fo B cells are presented in Table_S1_DEG.xlsx and Table_S2_DEG.xlsx file, respectively. KO versus Control fold changes, p-values, read counts and FPKM values for each sample are also shown in Table S1_DEG.xlsx and Table S2_DEG.xlsx files.

molecule: total RNA

organism: Mus musculus

source_name: B-1a cell

extract_protocol:
B-1a (IgM+, CD19+, CD5+, CD43+) and Fo B (B220+, CD93-, CD23+, CD21lo-mid) cells were isolated from the spleen by FACS-sorting using a MoFlo-XDP (Beckman Coulter). Total RNA was extracted using TRIzol Reagent (GeneAll, Seoul, Republic of Korea) according to the manufacturer's protocol.
DNA library for mRNA sequencing was prepared using a SMART-seq v4 Ultra Input RNA Kit (Clontech, for B-1a cells) and TruSeq RNA Sample Prep Kit v2 (Illumina, for Fo B cells), according to the manufacturer’s protocols. Libraries were sequenced on the Illumina Hiseq 4000 sequencer.

tag: genotype

value: Splenic B-1a cells

tag: age

value: 12 weeks


title: BS7.8_Clr1_t3_R2


title: BS7.8_Clr1_t3_R1


title: Capture Sequencing of 170kb Enhancers + SynHoxA assemblon delivered to WT mESC

value: 170kb Enhancers + SynHoxA assemblon in WT  mESCs

value: 170kb Enhancers + SynHoxA BAC


title: BS7.8_Clr1_t1_R1


title: BS7.8_Clr1_t2_R2


title: BS7.8_Clr1_SS_R2


title: BS7.8_Clr1_t1_R2


title: BS7.8_Clr1_ex_R2


title: JK2.8_Clr4_t1_R1

value: JK2.8 ([delta]ku80,[delta]clr4)


title: BS6.4_Clr2_t4_R1

value: BS6.4 ([delta]ku80,[delta]clr2)

value: t4= 4 h after spiking cellulose in steady state

value: replicate 1


title: BS7.8_Clr1_SS_R1

value: steady state-glucose


title: BS6.4_Clr2_t4_R2

value: replicate 2


title: BS6.4_Clr2_t2_R1


title: BS6.4_Clr2_t2_R2


title: BS6.4_Clr2_t1_R2


title: BS6.4_Clr2_SS_R2


title: BS6.4_Clr2_ex_R2


title: BS6.4_Clr2_t3_R1

value: t3= 2 h after spiking cellulose in steady state


title: BS6.4_Clr2_ex_R1


title: MJK20.3_Parental_t4_R2

value: MJK20.3 ([delta]ku80)


title: MJK20.3_Parental_t3_R2


title: BS6.4_Clr2_t1_R1


title: MJK20.3_Parental_t4_R1


title: MJK20.3_Parental_t3_R1


title: BS6.4_Clr2_SS_R1


title: MJK20.3_Parental_t2_R2


title: MJK20.3_Parental_t2_R1


title: BS7.8_Clr1_t2_R1


title: MJK20.3_Parental_t1_R1


title: MJK20.3_Parental_SS_R2


title: MJK20.3_Parental_t1_R2


title: MJK20.3_Parental_ex_R2


title: MJK20.3_Parental_SS_R1


title: MJK20.3_Parental_ex_R1


title: BS7.8_Clr1_ex_R1


title: BS6.4_Clr2_t3_R2


title: Lactobacillus rhamnosus ATCC 53103-Ribo-seq data-CG

city: Harbin

first: Zhen

last: Feng

state: Heilongjiang

address: Changjiang road 600

institute: Northeast Agricultural University

description: all.genes.expression.annot.txt

data_processing:
Library strategy: Ribo-seq
Prepared cDNA libraries were tested with Agilent 2100 bio analyzer for quality determination and then subjected to sequencing for quality determination and then subjected to sequencing with 50-bp single end using Illumina Hiseq 2000.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include count and FPKM values for each Sample

organism: Lacticaseibacillus rhamnosus GG

source_name: yogurt

growth_protocol: L. rhamnosus ATCC 53103 was obtained from the American Type Culture Collection (Manassas, VA). Cultures were stored at -80 ℃ in MRS medium containing 10% glycerol. The strain was revitalized in MRS broth at 37 ℃ for 12 h three times before use.

extract_protocol:
L. rhamnosus ATCC 53103 lysate was prepared following the protocols described previously with minor modifications. Cultures were poured onto chipped ice of the same volume and centrifuged at 4000 × g for 10 min at 4 ℃ for harvest. The resulting cell pellet was washed using 10 ml resuspension buffer [10 mM MgCl2, 100 mM NH4Cl, 20 mM Tris-HCl (pH 8.0) and 1mM chloramphenicol], and centrifuged again at 3000 × g for 5 min at 4 ℃. Cell pellet of each sample was then resolved in 2 ml lysis buffer [20 Mm Tris-HCl (pH 8.0), 100 mM NH4Cl, 10 mM MgCl2, 0.4% Triton X-100, 0.1% NP-40, 100 U/ml of RNase-free DNase Ⅰ (Roche), 0.5 U/µl of SUPERase In RNase inhibitor (Ambion) and 1 mM chloramphenicol]. Resuspended cells were poured over liquid nitrogen in 50 ml tubes, which were prepared with holes on the cap punched by a syringe needle. Then the tubes were placed at -80 ℃ for 30 min for nitrogen evaporation. Frozen cell pellets were pulverized using Freezer/Mill 6770 with the speed of impactor at 10 cycles per second for 2 min in two sets, transferred to a 50 ml tube, and stored at -80 ℃. After nitrogen evaporation, pulverized cells in 50-ml tubes were placed in water bath at 30 ℃ for immediate thaw, after which the cells were kept on ice for 10 min, and then transferred into a 1.5 ml Eppendorf tube. Lysate was aliquoted into 200 µl fractions, and flash frozen by liquid nitrogen and stored at -80 ℃ prior to further use.
50 µl or the cell lysate per sample was used to isolate total mRNAs with Gene JETRNA purification kit (Thermo Fisher Scientific, K0731). The rRNA removal for 5 µg total mRNAs was accomplished using the Ribo-ZeroTM MagneticKit for Gram-negative bacteria (Epicentre, MRZGN126). Afterward, RNAs were purified with RNA Clean & Concentrator kit (Zymo Research, R1015).RPFs from 100 µl lysate per sample were extracted as previously described. Notably, the concentration of Mg2+ in the lysate was supplemented to 15 mM to decrease the dissociation of 70S ribosomes. Clarified lysate was digested using 60 U MNase per one A260 unit of RNA with 5 mM CaCl2 in the reaction system, rotated at 1400 × g for 1 h at 25 ℃ in a thermomixer. The digestion was quenched with 6 mM EGTA. RPFs were isolated with Sephacryl S400 (GE, MicroSpin S-400 HR, 27514001) and purified using Acid Phenol: Chloroform extraction method prior to storage at -80 ℃ for further use. cDNA libraries of total mRNA and RPFs were constructed using the ARTseqTM Ribosome Profiling Kit (Epicentre, RPHMR12126) with different index tag at the reverse primers listed in Table X. Other primers used during the cDNA library construction were same as mentioned in the ARTseq Ribosome Profiling Kit (Epicentre RPHMR12126).
Prepared cDNA libraries were tested with Agilent 2100 bio analyzer for quality determination and then subjected to sequencing for quality determination and then subjected to sequencing with 50-bp single end using Illumina.

treatment_protocol: The growth of L. rhamnosus ATCC 53103 was monitored by automatic growth curve analyzer (Bioscreen Cpro; OY Growth Curves, Finland) at 600 nm (OD600). L. rhamnosus ATCC 53103 was growth in MRS broth at 37 ℃. The cells were harvested when the OD600 reached 1.8 by centrifugation (6000 × g, 10 min, 4 ℃). Then the cells were resuspended in two kinds of MRS broths which containing 0.0 and 0.6 M sodium lactate, respectively. For acid stress, the cells were collected when the OD600 reached 1.8 by centrifugation (6000 × g, 10 min, 4 ℃) and then resuspended in MRS medium (pH 5.0). The effect of acid stress on cell growth was further monitored. The effect of osmotic stress on cells growth was further monitored. Added 200 µg/ml chloramphenicol into the cultures when OD600 reached ~1.0, and then harvested cells after shaking for 2 min.

value: whole cells

tag: treatment

value: untreated was control group (CG)

tag: fraction

value: RPFs


title: Lactobacillus rhamnosus ATCC 53103-Ribo-seq data-OS2

description: all.genes.expression.annot.txt

value: treated with osmotic stress (OS)


title: Lactobacillus rhamnosus ATCC 53103-Ribo-seq data-OS1

description: all.genes.expression.annot.txt


title: Lactobacillus rhamnosus ATCC 53103-RNA-seq data-OS2

description: all.genes.expression.txt

data_processing:
Prepared cDNA libraries were tested with Agilent 2100 bio analyzer for quality determination and then subjected to sequencing for quality determination and then subjected to sequencing with 50-bp single end using Illumina Hiseq 2000.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include count and FPKM values for each Sample

value: total mRNAs


title: Lactobacillus rhamnosus ATCC 53103-RNA-seq data-CG

description: all.genes.expression.txt


title: Lactobacillus rhamnosus ATCC 53103-RNA-seq data-OS1

description: all.genes.expression.txt


title: SAMPLE 31

type: RNA

city: Guilin

first: deng

last: zhang

address: No. 85, Yanshan street, Yanshan District, Guilin, Guangxi

institute: Guangxi Institute of Botany

data_processing:
For the normalization it uses the most stable reference genes
For the normalization it uses combinations of the most stable reference genes
For the normalization it uses the least stable reference genes
Matrix normalized worksheet reports normalized signal (against housekeeping genes)

label: SYBR Green

organism: Arundo donax

source_name: Test

label_protocol: RT-qPCR amplification was performed in the Applied Biosystems Stepone system (Thermo, USA). The real-time PCR volume of 10 µL contained 5 µL 2X SYBR® Green Pro Taq HS Premix (Accurate Biology, China), 0.5 µL primer F (5 µmol·L−1), 0.5 µL primer R (5 µmol·L−1), 1.5 µL cDNA, 2.3 µL ddH2O, and 0.2 µL Reference Dye. RT-qPCR conditions were set as follows: 95 °C for 30 s, 40 cycles (95 °C for 5 s, 60 °C for 30 s), and an infinite hold at 10 °C. The melting curves ranging from 60 °C to 95 °C were evaluated in each reaction to confirm the specificity of amplified products.

extract_protocol: the total RNA from each sample was isolated using the SteadyPure Universal RNA Extraction Kit

value: Alkali treatment

value: leaves

tag: time


title: SAMPLE 32


title: SAMPLE 30


title: SAMPLE 22

value: Drought treatment


title: SAMPLE 29


title: SAMPLE 27

value: roots


title: SAMPLE 25


title: SAMPLE 16


title: SAMPLE 28


title: SAMPLE 23


title: SAMPLE 21


title: SAMPLE 14


title: SAMPLE 18


title: SAMPLE 26


title: SAMPLE 11

value: Salt treatment


title: SAMPLE 12


title: SAMPLE 13


title: SAMPLE 19


title: SAMPLE 17


title: SAMPLE 10


title: SAMPLE 15


title: SAMPLE 9


title: SAMPLE 8


title: SAMPLE 5


title: SAMPLE 6


title: SAMPLE 4


title: SAMPLE 24


title: SAMPLE 3


title: SAMPLE 20


title: SAMPLE 2

source_name: Control

value: No treatment

value: 0 h


title: SAMPLE 7


title: SAMPLE 1


title: Tumor9_(LNM-)

first: Yamin

last: Zhang

address: Kaixuan Road

institute: Zhejiang University

data_processing:
Illumina X Ten used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
FPKM values were calculated.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: genes_fpkm_expression.txt: Matrix table with raw gene counts and FPKM values for every gene and every sample.

source_name: Tumor tissue

extract_protocol:
Mucus and blood were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: diagnosis

value: oral squamous cell carcinoma (OSCS) without lymph-node metastasis (LNM)

value: Tumor tissue (Buccal mucosa)

tag: gender

value: Female

tag: patient age

tag: tumor stage

tag: grade

value: well


title: Tumor5_(LNM-)

value: medium


title: Tumor6_(LNM-)


title: Tumor3 _(LNM+)

value: oral squamous cell carcinoma (OSCS) with lymph-node metastasis (LNM)

value: Tumor tissue (Tongue)

value: Male


title: Tumor7_(LNM+)


title: Tumor4_(LNM-)

value: Tumor tissue (Gingiva)


title: A549 cells, TFAM_OE_1st

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Qvalue < =0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene read counts and  FPKM values for each Sample

source_name: A549 cell lines

growth_protocol: The A549 cells were ground into fine powder before RNA extraction.

extract_protocol:
For each sample, 1μg of the total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80C before sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Total RNA was extracted with TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.

tag: cell line

value: TFAM overexpression in A549 cell


title: Tumor8_(LNM+)

value: Tumor tissue (Mouth floor)

value: poor


title: BaseMeoh_1

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

description:
Sample name: S.279.1.d290139
dalvie090221_intCt.txt.gz
dalvie090221_l2cpm.txt.gz
transcriptome target: phaffi_transcripts_plusTransgenes011021.fa.gz

data_processing:
Sequencing using v3 chemistry. Software: Control v2.2.0.4, RTA 2.4.11. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
3’ DGE FASTQ sequencing reads were collapsed to one representative per unique molecular identifier using a custom script. Gene expression was quantified using salmon (version 1.3.0, Patro et al., 2017) using phaffi_transcripts_plusTransgenes011021.fa as a selective alignment target.  The resulting counts were summarized to the gene level using tximport (version 1.12.3) and counts per million (cpm) were calculated using utilities implement in edgeR (version 3.26.8, Chen et al., 2014). The cpm values with a +1 offset were transformed to log2 space for visualization.
Genome_build: Komagataella phaffi WT (PRJNA304977) with transcriptome phaffi_transcripts_plusTransgenes011021.fa
Supplementary_files_format_and_content: phaffi_transcripts_plusTransgenes011021.fa.gz is the fasta transcriptome file
Supplementary_files_format_and_content: dalvie090221_intCt.txt.gz is tab delimited integer count data prepared using the phaffi_plus_transgenes_020821.fa.gz target
Supplementary_files_format_and_content: dalvie090221_l2cpm.txt.gz is tab delimited counts per million with a plus 1 offset prepared using the phaffi_plus_transgenes_020821.fa.gz target

organism: Komagataella phaffii

source_name: bulk yeast cell culture

growth_protocol: Strains were grown in 3 mL culture in 24-well deep well plates (25°C, 600 rpm). Cells were cultivated in Rich Defined Media, described previously (Matthews et al., 2018). Cells were inoculated at 0.1 OD600, outgrown for 24 h with 4% glycerol feed, pelleted, and resuspended in fresh media with methanol or sorbitol feed to induce recombinant gene expression.

extract_protocol:
RNA was extracted and purified according to the Qiagen RNeasy kit (cat #74104) and RNA quality was analyzed to ensure RNA Quality Number >6.5.
3'DGE Nextera

treatment_protocol: Cells were inoculated at 0.1 OD600, outgrown for 24 h with 4% glycerol feed, pelleted, and resuspended in fresh media with 5% methanol or 4% sorbitol to induce recombinant gene expression.

tag: transgene

value: engineered SARS-Cov2 receptor binding domain RBD-B

tag: media supplement

value: 5% MeOH


title: BaseMeoh_2

description:
Sample name: S.279.2.d290140
dalvie090221_intCt.txt.gz
dalvie090221_l2cpm.txt.gz
transcriptome target: phaffi_transcripts_plusTransgenes011021.fa.gz


title: Mit1Sorb rep2

description:
Sample name: S.377.2.d290161
dalvie090221_intCt.txt.gz
dalvie090221_l2cpm.txt.gz
transcriptome target: phaffi_transcripts_plusTransgenes011021.fa.gz

value: 4% Sorbitol


title: BaseMeoh_3

description:
Sample name: S.279.3.d290141
dalvie090221_intCt.txt.gz
dalvie090221_l2cpm.txt.gz
transcriptome target: phaffi_transcripts_plusTransgenes011021.fa.gz


title: Tumor1 _(LNM+)

tag: tissue


title: Tumor2 _(LNM+)


title: A549 cells, TFAM_OE_2nd


title: Mit1Sorb rep1

description:
Sample name: S.377.1.d290160
dalvie090221_intCt.txt.gz
dalvie090221_l2cpm.txt.gz
transcriptome target: phaffi_transcripts_plusTransgenes011021.fa.gz


title: A549 cells, Ctrl_2nd

value: A549 cell (control plasmid)


title: A549 cells, Ctrl_3rd


title: A549 cells, TFAM_OE_3rd


title: Mit1Sorb rep3

description:
Sample name: S.377.3.d290162
dalvie090221_intCt.txt.gz
dalvie090221_l2cpm.txt.gz
transcriptome target: phaffi_transcripts_plusTransgenes011021.fa.gz


title: A549 cells, Ctrl_1st


title: ADC-Mech-Pre

city: Ratchathewi

first: Varodom

last: Charoensawan

state: Bangkok

address: 272 Thanon Rama VI

department: Biochemistry

country: Thailand

institute: Faculty of Science, Mahidol University

data_processing:
Reads alignment, filtering, barcode counting, and UMI counting were performed using the CellRanger software version 3.0.1 (10x Genomics, USA) with default parameters.
Data were quality controlled using the following inclusion criteria: genes per cell > 200, mitochondrial genes < 20%; SoupX was used for corrected for ambient RNA (https://github.com/constantAmateur/SoupX), normalised by sctransform, and integrated using Seurat v.3.1.2  using the standard workflow as described in www.https://satijalab.org/seurat/
Cells were clustered and projected on UMAP, then annotated based on canonical gene markers into epithelial cells (EPCAM, KRT8), fibroblast (SPARC, COL3A1), myeloid cells (S100A8, CD14), and other mixed lymphocytes (PTPRC, CD3E, NKG7)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited files of UMI counts of all cells and epithelial cells.
Supplementary_files_format_and_content: tab-delimited files of metadata of all cells and epithelial cells.

source_name: Ascites-derived cells

extract_protocol:
Ascites-derived cells were prepared for single-cell RNA-seq using the 10x Genomics Chromium Single Cell 3’ v2 (10x Genomics, PN-120267) according to the manufacturers protocol
Libraries were prepared for sequencing according to the 10x protocol (3' v2), and were sequenced with Illumina HiSeq platform with the 150PE sequencing format

tag: preperation method

value: Mechanical preparation

value: pre-treatment


title: ADC-Mech-Post

value: post-treatment


title: ADC-Enz-Post

value: Enzymatic preparation


title: ADC-Enz-Pre


title: DLD1 p85β K477A/R478A mutant cells RNA-Seq Rep3

city: Shanghai

first: Baoyu

last: He

address: No. 25, Lane 2200, Xietu Road

institute: Renji Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the (TPM) method. RSEM v1.3.1 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.24.0
Genome_build: hg18
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt

source_name: DLD1 p85β K477A/R480A mutant cells

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

value: colon

value: p85{beta} K477A/R478A mutant


title: DLD1 parental cells RNA-Seq Rep2

source_name: DLD1 parental cells

value: parental


title: DLD1 parental cells RNA-Seq Rep3


title: DLD1 p85β K477A/R478A mutant cells RNA-Seq Rep2

source_name: DLD1 p85β K477A/R479A mutant cells


title: siTTK_2

city: jinan

first: Gonghua

last: Qi

state: State...

address: 107 wenhua xi road

department: Department of Obstetrics and Gynecology

institute: shandong university

data_processing:
Sequenced reads were generated by base calling using the Illumina standard pipeline.
Raw reads were first filtered to obtain clean reads using FASTX-Toolkit.
High-quality reads were mapped to the human reference genome hg19 using TopHat software with default parameters.
Alignment was independently performed for reads from each sample, and reads mapping to more than three genomic sites were discarded.
Based on the value of reads per kilobase per million mapped reads, gene expression levels were determined using Cufflinks software.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Group.siTTK_vs_NC.degene_analysis.annot: Tab-delimited text file includes FPKM values.

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: serous ovarian cancer cell line

tag: sirna

value: si-TTK


title: DLD1 parental cells RNA-Seq Rep1


title: NC_1

tag: cell type

value: si-NC


title: siTTK_1


title: DLD1 p85β K477A/R478A mutant cells RNA-Seq Rep1

source_name: DLD1 p85β K477A/R478A mutant cells

tag: genotype


title: NC_2


title: OVCAR3_BORIS_OE_rep2

city: Mexico City

first: Ernesto

last: Soto-Reyes

state: Mexico City

address: Av. Vasco de Quiroga

department: Departamento de Ciencias Naturales

country: Mexico

institute: Universidad Autónoma Metropolitana

data_processing:
Reads were preprocessed with Trimmomatic to remove low quality reads and adapters.
Pseudoalignment to transcriptome was performed with Kallisto using the Human reference transcriptome (GRCh38, Ensembl release 94)
Counts were obtained with FeatureCounts from the R package Rsubread v1.32.4
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: The human epithelial ovarian cancer cell line OVCAR3 was subcultured in complete growth medium contained RPMI-1640 Medium, supplemented with 20% fetal bovine serum and 0.01 mg/ml bovine insulin and incubated at 37ºC and at 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol Reagent and Direct-zol RNA Miniprep.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: OVCAR3 cell lines with CTCFL (BORIS) overexpression were obtained with transient transfection of the plasmid pCpGfree-vitroHBORIS which contains the CTCFL ORF encoding the canonic protein of 663 amino acids, the construct was donated by Prof. Lobanenkov and Dr. Pugacheva. Briefly, OVCAR3 cells grown to 70% density were transiently transfected with pCpGfree-vitroHBORIS using Xfect Transfection Reagent and 2 µg of plasmid, transfections were performed overnight. Cells were collected 48 h post-transfection for RNA and protein extraction. Knowckdown of CTCFL (BORIS) was achieved as described in Salgado-Albarran et al. (PBMID: 31406110). For each treatment, three technical replicates were pooled together to obtain one biological replicate. Three independent biological replicates were performed per condition.

value: Overexpression


title: siTTK_3


title: NC_3


title: OVCAR3_BORIS_KD_rep1

value: Underexpression


title: OVCAR3_BORIS_OE_rep1


title: OVCAR3_CONTROL_rep2


title: OVCAR3_BORIS_OE_rep3


title: OVCAR3_CONTROL_rep3


title: OVCAR3_BORIS_KD_rep3


title: OVCAR3_BORIS_KD_rep2


title: SKBR3_2

city: Seoul

first: Jungmin

last: Choi

state: Seoul

address: 73, Goryeodae-ro, Seongbuk-gu

department: Department of Biomedical Sciences

institute: Korea University College of Medicine

data_processing:
alignment of reads using bowtie2 (ver2.2.4)
peak calling using MACS2 (ver2.1.1)
Genome_build: hg19
Supplementary_files_format_and_content: excel files and peak information

growth_protocol: SKBR3 cells were maintained in culture in DMEM +GlutaMAX-1 (Gibco-life Technologies) containing 10% fetal bovine serum (FBS) and pen/strep (Gibco-life Technologies) at 37˚C in 5% CO2.

extract_protocol:
Genomic DNAs were extracted by DNA Clean & Concentrator (Zymo).
ATAC-seq libraries were constructed with 50K cells from each condition following Omni-ATAC protocol (Illumina 20034197(Corces et al., 2017))

value: Breast cancer cells

value: HER2 positive


title: OVCAR3_CONTROL_rep1


title: SKBR3_1


title: RNA-seq_WBC_sample14

city: Pieve Emanuele

first: Elvezia

middle: Maria

last: Paraboschi

address: via Rita Levi Montalcini 4

country: Italy

institute: Humanitas University

data_processing:
Sequencing reads were mapped to the human genome (hg19) using STAR (version 2.5.2)
Transcript quantification from mapped reads was performed using HTSeq-count (version 0.6.1p1) and the human transcripts annotations from Ensembl database (GRCh37 version)
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: blood

extract_protocol:
Whole blood was collected in a PAXgene Blood RNA Tube (PreAnalytiX, Switzerland) and RNA extraction performed using the Maxwell simplyRNA Blood Kit (Promega, USA), following the manufacturer's instructions.
Libraries were prepared starting from 500 ng of total RNA, using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and following the manufacturer's instructions. Samples underwent a paired-end 75 bp sequencing using a NextSeq 500 platform (Illumina)

tag: disease state

value: not affected

value: blood cells


title: RNA-seq_WBC_sample11


title: RNA-seq_WBC_sample13

value: affected


title: RNA-seq_WBC_sample8


title: RNA-seq_WBC_sample9


title: RNA-seq_WBC_sample12


title: RNA-seq_WBC_sample7


title: RNA-seq_WBC_sample6


title: RNA-seq_WBC_sample5


title: RNA-seq_WBC_sample4


title: RNA-seq_WBC_sample1


title: RNA-seq_WBC_sample3


title: RNA-seq_WBC_sample2


title: RNA-seq_WBC_sample10


title: thymic_immatDNNKT_rep4

city: Townsville

first: Margaret

middle: Agnes

last: Jordan

state: QLD

address: The Science Place, James Cook Dr

department: Molecular & Cell Biology

country: Australia

institute: James Cook University

description: sample isolated from single mouse

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17+/- 1 hr at 45C on Affymetrix Mouse Gene_1.0ST arrays. GeneChips were washed and stained using the GeneChip Hybridization Wash and Stain Kit (Affymetrix, CA, USA) in the Affymetrix Fluidics Station 450 using AGCC Fluidics control software.

scan_protocol: Gene chips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: Images (.dat files) were processed using GeneChip Command Console (Affymetrix, CA, USA) and CEL files imported into Partek Genomics Suite 6.6 (Partek SG, Singapore) for further analysis following RMA summarisation. For gene co-expression network construction, Affymetrix CEL files were normalized using RMA background subtraction in Bioconductor and batch effects were removed using the nonparametric CombatR algorithm. Variability of transcripts across all arrays was ranked by standard deviation and the 1,929 most variable were used for network construction.

label: biotin

source_name: Mouse thymic (TCR+ CD1d-tet+ DN CD24+ NK1.1- ) cells

label_protocol: Biotinylated cRNA were prepared according to the Two-Cycle Target Labeling Assay of the Affymetrix protocol from 100ng total RNA (Expression Analysis Technical Manual, 2004, Affymetrix)

growth_protocol: pure isolated cells used, not grown

extract_protocol: Sorted immature thymic T and NKT cell subsets (7 samples/group) were individually homogenized in the RLT buffer of an RNeasy kit (QIAGEN, Venlo, Limburg, Netherlands); homogenates were passed through QIAshedder columns (QIAGEN, Limburg, Netherlands) and extracted (RNeasy; QIAGEN, Limburg, Netherlands). The RNA yield was quantified spectrophotometrically on a Nanodrop ND-1000 and aliquots electrophoresed for determination of sample concentration and purity. Samples were concentrated using Microcons to ensure a concentration at least 33.3ng /ul.

treatment_protocol: no treatment

tag: strain

tag: age

value: 6 weeks

value: thymus


title: thymic_immatDPNKT_rep1

description: sample isolated from single mouse

source_name: Mouse thymic (TCR+ CD1d-tet+ CD4+ CD8+ CD24+ NK1.1- ) cells


title: thymic_immatDPNKT_rep6

description: sample isolated from single mouse

value: thymic (TCR+ CD1d-tet+ CD4+ CD8+ CD24+ NK1.1- ) cells


title: thymic_DP thymocyte_rep4

description: sample isolated from single mouse

source_name: Mouse thymic (TCR+ CD1d-tet- CD4+ CD8+ CD24+ NK1.1- ) cells


title: PC_3

city: Portland

first: Jessica

last: Minnier

state: OR

address: 3181 SW Sam Jackson Park Rd, UHN62

institute: Oregon Health & Science University

data_processing:
Input sequences were 101bp mouse samples, except for pericytes which were 70bp single-end due to sequencer malfunction
EC_1 and PC samples were single end, all other samples are paired-end
Illumina Casava was used to assemble fastq files
percitye samples and smooth muscle cell samples were aligned together after trimming SMC to 70bp. Endothelial samples were aligned separately.
Trimming of known adapters and low-quality regions of reads was performed using Fastq-mcf
Sequence quality control was assessed using the program FastQC
Alignment of the provided samples to the mm9 whole genome was performed using the Subread aligner
Reads were assigned to genes using the program "featureCounts", part of the Subread R package
Reads that were aligned uniquely to reference sequence were used for further analyses; Tags with < 0.5 cpm in at least 2 samples were excluded.
TMM normalization was performed with edgeR and log2cpm values were calculated
Genome_build: mm9
Supplementary_files_format_and_content: comma-delimited text file (csv) includes multiple gene identifiers, read counts, normalized CPM values for each sample, and average log2cpm by each sample type

source_name: adult mouse heart microvascular cells

extract_protocol:
RNA was extracted from confluent cultures of endothelial cells, pericytes and vascular smooth muscle cells (1 T75 flask/ sample), using Triazol (Invitrogen) followed by RNAeasy universal mini RNA kit, according to manufacturer’s instructions.
PolyA(+) RNA is isolated using oligo-dT bound to magnetic beads.  Recovered RNA is chemically fragmented to about 200-300 bp.  Double stranded cDNA is made from the fragmented RNA using random hexamer priming.  The double stranded cDNA product is treated to “blunt” the ends.  A single “A” base is added to the ends of the fragments.  Proprietary Illumina adaptors are attached to the fragments by ligation. The unique “Y” structure of the adaptors ensures that different oligonucleotides are on the end of each strand.  The library is amplified by a limited number (usually 12) rounds of polymerase chain reaction.  The amplified library is cleaned using AMPure XP beads (Agencourt), then run on the Bioanalyzer (Agilent) to ensure that library preparation has been successful.  Sequenced 100 cycle single read on the HiSeq 2000.  Data was converted to fastq files with CASAVA (Illumina).

tag: sequencing id

value: heart pericytes


title: thymic_DP thymocyte_rep5

description: sample isolated from single mouse

value: thymic (TCR+ CD1d-tet- CD4+ CD8+ CD24+ NK1.1- ) cells


title: thymic_DP thymocyte_rep3

description: sample isolated from single mouse


title: thymic_immatDNNKT_rep7

description: sample isolated from single mouse

value: thymic (TCR+ CD1d-tet+ DN CD24+ NK1.1- ) cells


title: thymic_immatDPNKT_rep3

description: sample isolated from single mouse


title: thymic_DP thymocyte_rep2

description: sample isolated from single mouse


title: thymic_immatDNNKT_rep3

description: sample isolated from single mouse


title: thymic_DP thymocyte_rep1

description: sample isolated from single mouse


title: thymic_immatDPNKT_rep4

description: sample isolated from single mouse


title: thymic_DP thymocyte_rep7

description: sample isolated from single mouse


title: thymic_DP thymocyte_rep6

description: sample isolated from single mouse


title: thymic_immatDNNKT_rep2

description: sample isolated from single mouse


title: thymic_immatDPNKT_rep2

description: sample isolated from single mouse


title: PC_2


title: thymic_immatDNNKT_rep6

description: sample isolated from single mouse


title: thymic_immatDPNKT_rep5

description: sample isolated from single mouse


title: thymic_immatCD4NKT_rep7

description: pooled sample of immat CD4NKT cells from three mice

source_name: Mouse thymic (TCR+ CD1d-tet+ CD4+ CD8- CD24+ NK1.1- ) cells


title: thymic_immatCD4NKT_rep3

description: sample isolated from single mouse

value: thymic (TCR+ CD1d-tet+ CD4+ CD8- CD24+ NK1.1- ) cells


title: thymic_immatCD4NKT_rep2

description: sample isolated from single mouse


title: thymic_immatDPNKT_rep7

description: sample isolated from single mouse


title: thymic_immatCD4NKT_rep5

description: sample isolated from single mouse


title: thymic_immatDNNKT_rep1

description: sample isolated from single mouse


title: thymic_immatDNNKT_rep5

description: sample isolated from single mouse


title: VSMC_3

value: heart smooth muscle cells


title: PC_1


title: thymic_immatCD4NKT_rep1

description: sample isolated from single mouse


title: VSMC_1


title: thymic_immatCD4NKT_rep6

description: sample isolated from single mouse


title: VSMC_2


title: EC_3

value: heart endothelial cells


title: thymic_immatCD4NKT_rep4

description: pooled sample of immat CD4NKT cells from two mice


title: EC_2


title: EC_1


title: NZB-F2_Liver_R2_001

city: New York

first: Edmund

middle: C

last: Jenkins

state: NY

address: 1468 Madison Avenue

department: Heme/Onc

institute: Icahn School of Medicine at Mt. Sinai

data_processing:
raw FASTQ files were aligned using Biojupies ( https://amp.pharm.mssm.edu/biojupies/ )
Supplementary_files_format_and_content: Matrix table with noralized gene counts for every gene and every sample
Supplementary_files_format_and_content: Files names and experimental groups
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: BL6 NZB liver

extract_protocol:
Flash froze tissue sent to Genewiz
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tag

value: liver

tag: Sex

value: female


title: NZB-F3_Liver_R2_001


title: NZB-F3_Liver_R1_001


title: C57-M3_Liver_R1_001

source_name: BL6C57 liver

value: male


title: NZB-F4_Liver_R2_001


title: C57-M4_Liver_R2_001


title: C57-M4_Liver_R1_001


title: NZB-F1_Liver_R1_001


title: NZB-F2_Liver_R1_001


title: NZB-F1_Liver_R2_001


title: C57-M3_Liver_R2_001


title: NZB-F4_Liver_R1_001


title: NZB-M4_Liver_R2_001


title: NZB-M3_Liver_R1_001


title: NZB-M1_Liver_R2_001


title: NZB-M2_Liver_R1_001


title: NZB-M4_Liver_R1_001


title: C57-M2_Liver_R2_001


title: C57-F4_Liver_R2_001


title: C57-F4_Liver_R1_001


title: C57-F3_Liver_R1_001


title: NZB-M2_Liver_R2_001


title: NZB-M3_Liver_R2_001


title: C57-M2_Liver_R1_001


title: NZB-M1_Liver_R1_001


title: C57-F2_Liver_R1_001


title: C57-F2_Liver_R2_001


title: C57-F1_Liver_R2_001


title: H3.3WT NSC rep 2

city: Ann Arbor

first: Sriram

last: Venneti

state: MI

address: 1150 W. Medical Center Drive

department: Department of Pathology

institute: University of Michigan

data_processing:
fastq files were aligned to mouse reference genome mm10 using bowtie and analyzed using RSEM software
Differentially expressed genes (£5% false discovery rate) were identified by Bayesian hierarchical models (statistics using the Limma package
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample ...

source_name: mouse neuronal stem cells

growth_protocol: 5x106 NSCs/well were plated in T75 tissue culture flasks and placed in a 5% CO2 37 °C incubator

extract_protocol:
RNA was isolated using TRIzol and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Protocol, according to the manufacturer’s instructions, and sequenced on an Illumina HiSeq2000

tag: background strain

value: Blbp-eGFP transgenic mice

value: H3.3 wild type


title: H3.3WT NSC rep 1


title: H3.3K27M NSC rep 3


title: H3.3WT NSC rep 3


title: C57-M1_Liver_R1_001


title: H3G34R_H3K36me3

data_processing:
fastq files were aligned to mouse reference genome mm10 using the BWA algorithm
Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome
For active histone marks (H3K4me3 and H3K27ac), peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of p-value = 1e-7. For H3K27me3 enriched regions were identified using the SICER algorithm at a cutoff of FDR 1E-10 and a max gap parameter of 600 bp. Spike-in of Drosophila chromatin was performed and the number of test tags were normalized by the same number of spike-in Drosophila tags for each sample.
Genome_build: mm10
Supplementary_files_format_and_content: bw files for each histone mark in each NSC line expressing either H3.3WT, H3.3K27M, or H3.3G34R transgenes

source_name: H3.3G34R NSC

growth_protocol: 10x106 NSCs/well were plated in T75 tissue culture flasks and placed in a 5% CO2 37 °C incubator

extract_protocol:
Chromatin was isolated by the addition of lysis buffer and lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were re-suspended and the DNA was quantified on a NanoDrop spectrophotometer.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end). Reads were aligned to the mouse genome (mm10) using the BWA algorithm.

value: neuronal stem cells

tag: antibody


title: H3.3G34R NSC rep 2


title: C57-M1_Liver_R2_001


title: C57-F3_Liver_R2_001


title: H3WT_H3K27Ac

source_name: H3.3WT NSC


title: H3.3G34R NSC rep 1


title: H3.3K27M NSC rep 1


title: H3.3K27M NSC rep 2


title: H3K27M_H3K27me3

source_name: H3.3K27M NSC


title: H3.3G34R NSC rep 3


title: C57-F1_Liver_R1_001


title: H3K27M_H3K36me3


title: H3G34R_H3K4me3


title: H3WT_H3K27me3


title: H3WT_H3K36me3


title: H3WT_H3K4me3


title: H3K27M_H3K4me3


title: H3G34R_H3K27Ac


title: gDNA from relapse pediatric AML 1047

type: genomic

first: Soheil

last: Meshinchi

state: Washington

address: 1100 Fairview Ave N.

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

description:
pediatric AML
PAVRUZ_REL

hyb_protocol: Bisulfite-converted genomic DNA was analyzed using the Infinium Human Methylation EPIC Beadchip Kit (Illumina). DNA amplification, fragmentation, array hybridization, extension and staining were performed with reagents provided in the kit according to the manufacturer’s protocol (Illumina Infinium II Methylation Assay). Briefly, 4 µl of bisulfite-converted genomic DNA at a minimum concentration of 20 ng/µL) was added to 0.8 ml 96-well storage plate (Thermo Fisher Scientific), denatured in 0.014N sodium hydroxide, neutralized and then amplified for 20-24 hours at 37oC. Samples were fragmented at 37oC for 60 minutes and precipitated in isopropanol. Re-suspended samples were denatured in a 96-well plate heat block at 95oC for 20 minutes. 15 µl of each sample was loaded onto a 12-sample BeadChip, assembled in the hybridization chamber as instructed by the manufacturer and incubated at 48oC for 16-20 hours. Following hybridization, the BeadChips were washed and assembled in a fluid flow-through station for primer-extension reaction and staining with reagents and buffers provided.

scan_protocol: Polymer-coated BeadChips were scanned in an iScan scanner (Illumina) using Inf Methylation mode

data_processing:
DNA methylation profiling was performed at Arkansas Children’s Research Institute  on the Illumina Infinium HumanMethylationEPIC platform, using recommended manufacturer protocols. The resulting data were processed as recommended to match LAML, TARGET AML, and TARGET AML-IF HumanMethylation450 array results, then corrected for artifacts resulting from copy number alterations and differences in cellularity where estimates were available.  Raw IDAT files were processed using R package SeSAMe (PMID: 30085201) with noob background correction (PMID: 23476028, 28035024), non-linear dye bias correction, SNP and non-detection (p-value) masking. Methylation beta values are computed as the fraction of total probeset intensity attributable to fluorescence from the methylated probe allele, with 0 indicating no methylation and 1 indicating full methylation. The SeSAMe/noob default offset of 15 was added to both unmethylated (U) and methylated (M) allelic intensities in each pair to avoid division by zero. We excluded measurements from sub-optimally designed probes due to overlap with SNPs and repeat elements, as suggested by previous studies (PMID: 27924034).
Processed data file includes normalized (SeSAMe) Average Beta

label: Cy5 and Cy3

source_name: pediatric AML sample 1047

label_protocol: Bisulfite conversion of genomic DNA was performed with EZ DNA methylation Kit (Zymo Research, Irvine, CA, #D5002) following the manufacturer’s protocol with modifications for the Infinium Methylation Assay. Briefly, 250ng of genomic DNA was mixed with 5 µl of Dilution Buffer and incubated at 37oC for 15 minutes and then mixed with 100 µl of conversion reagent prepared as instructed in the protocol. Mixtures were incubated in a thermocycler for 16 cycles at 95oC for 30 seconds and 50oC for 60 minutes. Bisulfite-converted DNA samples were loaded onto the provided 96-column plates for desulphonation, washing and elution. The concentration of bisulfite-converted, eluted DNA was measured by UV-absorbance using a NanoDrop-1000 (Thermo Fisher Scientific, Waltham, MA)

extract_protocol: Starting with one vial of cryopreserved cells derived from Bone Marrow or Peripheral Blood, cells undergo a quick thaw and are adding to a tube containing PBS (to dilute the residual DMSO).  Cells are spun at 1000RPM and pelleted.  The pellet is vortexed and resuspended in lysis buffer from the Qiagen AllPrep DNA/RNA mini kit.  The lysate is added to an RNeasy spin column to isolate RNA while the flow through is added to the DNA spin column for subsequent DNA isolation.  After a series of washes on each column, DNA or RNA is eluted into a tube using elution buffer or RNase-free H20 respectively.  Both nucleic acids are evaluated on the NanoDrop for initial sample concentration and quality.  DNA quantification is then assessed using the Picogreen assay for better accuracy.  RNA quality and quantity is also assessed using the Agilent Bioanalyzer nanochip.

tag: trial protocol

tag: batch

value: Female

tag: age (years)

tag: timepoint

value: Relapse

tag: fusion


title: H3G34R_H3K27me3


title: gDNA from relapse pediatric AML 1046

description:
pediatric AML
PAWANV_REL

source_name: pediatric AML sample 1046

value: Male


title: H3K27M_H3K27Ac


title: gDNA from relapse pediatric AML 1042

description:
pediatric AML
PAULTY_REL

source_name: pediatric AML sample 1042


title: gDNA from relapse pediatric AML 1043

description:
pediatric AML
PAUVGD_REL

source_name: pediatric AML sample 1043


title: gDNA from relapse pediatric AML 1044

description:
pediatric AML
PAUVZD_REL

source_name: pediatric AML sample 1044


title: gDNA from relapse pediatric AML 1039

description:
pediatric AML
PAUSFM_REL

source_name: pediatric AML sample 1039


title: gDNA from relapse pediatric AML 1035

description:
pediatric AML
PAXLBH_REL

source_name: pediatric AML sample 1035


title: gDNA from relapse pediatric AML 1034

description:
pediatric AML
PAXMNR_REL

source_name: pediatric AML sample 1034


title: gDNA from relapse pediatric AML 1038

description:
pediatric AML
PAWHCT_REL

source_name: pediatric AML sample 1038


title: gDNA from relapse pediatric AML 1040

description:
pediatric AML
PAXLDI_REL

source_name: pediatric AML sample 1040


title: gDNA from relapse pediatric AML 1041

description:
pediatric AML
PAUUKZ_REL

source_name: pediatric AML sample 1041


title: gDNA from relapse pediatric AML 1037

description:
pediatric AML
PAXLVV_REL

source_name: pediatric AML sample 1037


title: gDNA from relapse pediatric AML 1036

description:
pediatric AML
PAXDSN_REL

source_name: pediatric AML sample 1036


title: gDNA from relapse pediatric AML 1032

description:
pediatric AML
PAXGHE_REL

source_name: pediatric AML sample 1032


title: gDNA from relapse pediatric AML 1033

description:
pediatric AML
PAXJAA_REL

source_name: pediatric AML sample 1033


title: gDNA from relapse pediatric AML 1026

description:
pediatric AML
PAXDDY_REL

source_name: pediatric AML sample 1026


title: gDNA from relapse pediatric AML 1031

description:
pediatric AML
PAWTWW_REL

source_name: pediatric AML sample 1031


title: gDNA from relapse pediatric AML 1029

description:
pediatric AML
PAVXEB_REL

source_name: pediatric AML sample 1029


title: gDNA from relapse pediatric AML 1028

description:
pediatric AML
PAXHPH_REL

source_name: pediatric AML sample 1028


title: gDNA from relapse pediatric AML 1024

description:
pediatric AML
PAWVCG_REL

source_name: pediatric AML sample 1024


title: gDNA from relapse pediatric AML 1045

description:
pediatric AML
PAUNYL_REL

source_name: pediatric AML sample 1045


title: gDNA from relapse pediatric AML 1023

description:
pediatric AML
PAWECG_REL

source_name: pediatric AML sample 1023


title: gDNA from relapse pediatric AML 1027

description:
pediatric AML
PAXIFA_REL

source_name: pediatric AML sample 1027


title: gDNA from relapse pediatric AML 1022

description:
pediatric AML
PAWHRR_REL

source_name: pediatric AML sample 1022


title: gDNA from relapse pediatric AML 1021

description:
pediatric AML
PAWCCR_REL

source_name: pediatric AML sample 1021


title: gDNA from relapse pediatric AML 1020

description:
pediatric AML
PAWEYY_REL

source_name: pediatric AML sample 1020


title: gDNA from relapse pediatric AML 1018

description:
pediatric AML
PAWDTX_REL

source_name: pediatric AML sample 1018


title: gDNA from relapse pediatric AML 1019

description:
pediatric AML
PAVGKS_REL

source_name: pediatric AML sample 1019


title: gDNA from relapse pediatric AML 1030

description:
pediatric AML
PAXCKK_REL

source_name: pediatric AML sample 1030


title: gDNA from relapse pediatric AML 1025

description:
pediatric AML
PAWKGX_REL

source_name: pediatric AML sample 1025


title: gDNA from relapse pediatric AML 1017

description:
pediatric AML
PAWIWJ_REL

source_name: pediatric AML sample 1017


title: gDNA from relapse pediatric AML 1016

description:
pediatric AML
PAVWNG_REL

source_name: pediatric AML sample 1016


title: gDNA from relapse pediatric AML 1015

description:
pediatric AML
PAVUGM_REL

source_name: pediatric AML sample 1015


title: gDNA from relapse pediatric AML 1011

description:
pediatric AML
PAVMEH_REL

source_name: pediatric AML sample 1011


title: gDNA from relapse pediatric AML 1012

description:
pediatric AML
PAVTRU_REL

source_name: pediatric AML sample 1012


title: gDNA from relapse pediatric AML 1013

description:
pediatric AML
PAVWRN_REL

source_name: pediatric AML sample 1013


title: gDNA from relapse pediatric AML 1006

description:
pediatric AML
PAVDHJ_REL

source_name: pediatric AML sample 1006


title: gDNA from relapse pediatric AML 1010

description:
pediatric AML
PAVWVT_REL

source_name: pediatric AML sample 1010


title: gDNA from relapse pediatric AML 1014

description:
pediatric AML
PAVVAT_REL

source_name: pediatric AML sample 1014


title: gDNA from relapse pediatric AML 1009

description:
pediatric AML
PAVVKU_REL

source_name: pediatric AML sample 1009


title: gDNA from relapse pediatric AML 1008

description:
pediatric AML
PAVGEV_REL

source_name: pediatric AML sample 1008


title: gDNA from relapse pediatric AML 1005

description:
pediatric AML
PAVDBT_REL

source_name: pediatric AML sample 1005


title: gDNA from relapse pediatric AML 1004

description:
pediatric AML
PAUPPD_REL

source_name: pediatric AML sample 1004


title: gDNA from relapse pediatric AML 1002

description:
pediatric AML
PAWHPL_REL

source_name: pediatric AML sample 1002


title: gDNA from relapse pediatric AML 1001

description:
pediatric AML
PAXLWH_REL

source_name: pediatric AML sample 1001


title: gDNA from relapse pediatric AML 1003

description:
pediatric AML
PAUTJD_REL

source_name: pediatric AML sample 1003


title: gDNA from relapse pediatric AML 997

description:
pediatric AML
PAXIJB_REL

source_name: pediatric AML sample 997


title: gDNA from relapse pediatric AML 995

description:
pediatric AML
PAXDEG_REL

source_name: pediatric AML sample 995


title: gDNA from relapse pediatric AML 999

description:
pediatric AML
PAWPVX_REL

source_name: pediatric AML sample 999


title: gDNA from relapse pediatric AML 998

description:
pediatric AML
PAXJMY_REL

source_name: pediatric AML sample 998


title: gDNA from relapse pediatric AML 1048

description:
pediatric AML
PAVKJD_REL

source_name: pediatric AML sample 1048


title: gDNA from relapse pediatric AML 996

description:
pediatric AML
PAWZZN_REL

source_name: pediatric AML sample 996


title: gDNA from relapse pediatric AML 994

description:
pediatric AML
PAXICE_REL

source_name: pediatric AML sample 994


title: gDNA from relapse pediatric AML 1000

description:
pediatric AML
PAWYEM_REL

source_name: pediatric AML sample 1000


title: gDNA from relapse pediatric AML 989

description:
pediatric AML
PAWKJC_REL

source_name: pediatric AML sample 989


title: gDNA from relapse pediatric AML 991

description:
pediatric AML
PAWTSD_REL

source_name: pediatric AML sample 991


title: gDNA from relapse pediatric AML 992

description:
pediatric AML
PAWYNR_REL

source_name: pediatric AML sample 992


title: gDNA from relapse pediatric AML 993

description:
pediatric AML
PAXJXC_REL

source_name: pediatric AML sample 993


title: gDNA from relapse pediatric AML 990

description:
pediatric AML
PAXMKT_REL

source_name: pediatric AML sample 990


title: gDNA from relapse pediatric AML 988

description:
pediatric AML
PAXISI_REL

source_name: pediatric AML sample 988


title: gDNA from relapse pediatric AML 1007

description:
pediatric AML
PAVCPM_REL

source_name: pediatric AML sample 1007


title: gDNA from relapse pediatric AML 987

description:
pediatric AML
PAXCYN_REL

source_name: pediatric AML sample 987


title: gDNA from relapse pediatric AML 986

description:
pediatric AML
PAXJFS_REL

source_name: pediatric AML sample 986


title: gDNA from relapse pediatric AML 985

description:
pediatric AML
PAXKEZ_REL

source_name: pediatric AML sample 985


title: gDNA from relapse pediatric AML 984

description:
pediatric AML
PAXELP_REL

source_name: pediatric AML sample 984


title: gDNA from relapse pediatric AML 982

description:
pediatric AML
PAXGIX_REL

source_name: pediatric AML sample 982


title: gDNA from relapse pediatric AML 983

description:
pediatric AML
PAWWCW_REL

source_name: pediatric AML sample 983


title: gDNA from relapse pediatric AML 981

description:
pediatric AML
PAWZVT_REL

source_name: pediatric AML sample 981


title: gDNA from relapse pediatric AML 979

description:
pediatric AML
PAXGGM_REL

source_name: pediatric AML sample 979


title: gDNA from relapse pediatric AML 980

description:
pediatric AML
PAXAXY_REL

source_name: pediatric AML sample 980


title: gDNA from relapse pediatric AML 975

description:
pediatric AML
PAWMFY_REL

source_name: pediatric AML sample 975


title: gDNA from relapse pediatric AML 973

description:
pediatric AML
PAWSHR_REL

source_name: pediatric AML sample 973


title: gDNA from relapse pediatric AML 978

description:
pediatric AML
PAWVGF_REL

source_name: pediatric AML sample 978


title: gDNA from relapse pediatric AML 974

description:
pediatric AML
PAWWXU_REL

source_name: pediatric AML sample 974


title: gDNA from relapse pediatric AML 976

description:
pediatric AML
PAWNPU_REL

source_name: pediatric AML sample 976


title: gDNA from relapse pediatric AML 969

description:
pediatric AML
PAUMUZ_REL

source_name: pediatric AML sample 969


title: gDNA from relapse pediatric AML 972

description:
pediatric AML
PAWUWJ_REL

source_name: pediatric AML sample 972


title: gDNA from relapse pediatric AML 971

description:
pediatric AML
PAUXNH_REL

source_name: pediatric AML sample 971


title: gDNA from relapse pediatric AML 963

description:
pediatric AML
PAXETC_REL

source_name: pediatric AML sample 963


title: gDNA from relapse pediatric AML 967

description:
pediatric AML
PAWNPG_REL

source_name: pediatric AML sample 967


title: gDNA from relapse pediatric AML 965

description:
pediatric AML
PAVZEC_REL

source_name: pediatric AML sample 965


title: gDNA from relapse pediatric AML 966

description:
pediatric AML
PAWPMA_REL

source_name: pediatric AML sample 966


title: gDNA from relapse pediatric AML 968

description:
pediatric AML
PAVTLN_REL

source_name: pediatric AML sample 968


title: gDNA from relapse pediatric AML 964

description:
pediatric AML
PAWSRG_REL

source_name: pediatric AML sample 964


title: gDNA from relapse pediatric AML 959

description:
pediatric AML
PAWWZL_REL

source_name: pediatric AML sample 959


title: gDNA from relapse pediatric AML 958

description:
pediatric AML
PAWXIA_REL

source_name: pediatric AML sample 958


title: gDNA from relapse pediatric AML 957

description:
pediatric AML
PAWMKP_REL

source_name: pediatric AML sample 957


title: gDNA from relapse pediatric AML 956

description:
pediatric AML
PAWNYX_REL

source_name: pediatric AML sample 956


title: gDNA from relapse pediatric AML 977

description:
pediatric AML
PAWZUZ_REL

source_name: pediatric AML sample 977


title: gDNA from relapse pediatric AML 954

description:
pediatric AML
PAWUAE_REL

source_name: pediatric AML sample 954


title: gDNA from relapse pediatric AML 953

description:
pediatric AML
PAWLYM_REL

source_name: pediatric AML sample 953


title: gDNA from relapse pediatric AML 952

description:
pediatric AML
PAWNHW_REL

source_name: pediatric AML sample 952


title: gDNA from relapse pediatric AML 970

description:
pediatric AML
PAVWBW_REL

source_name: pediatric AML sample 970


title: gDNA from relapse pediatric AML 949

description:
pediatric AML
PAWHKK_REL

source_name: pediatric AML sample 949


title: gDNA from relapse pediatric AML 960

description:
pediatric AML
PAWFRK_REL

source_name: pediatric AML sample 960


title: gDNA from relapse pediatric AML 962

description:
pediatric AML
PAWUTL_REL

source_name: pediatric AML sample 962


title: gDNA from relapse pediatric AML 948

description:
pediatric AML
PAWPKR_REL

source_name: pediatric AML sample 948


title: gDNA from relapse pediatric AML 945

description:
pediatric AML
PAWLEB_REL

source_name: pediatric AML sample 945


title: gDNA from relapse pediatric AML 943

description:
pediatric AML
PAUZVP_REL

source_name: pediatric AML sample 943


title: gDNA from relapse pediatric AML 942

description:
pediatric AML
PAVJXG_REL

source_name: pediatric AML sample 942


title: gDNA from relapse pediatric AML 947

description:
pediatric AML
PAWHTL_REL

source_name: pediatric AML sample 947


title: gDNA from relapse pediatric AML 961

description:
pediatric AML
PAWVGN_REL

source_name: pediatric AML sample 961


title: gDNA from relapse pediatric AML 937

description:
pediatric AML
PAVKAU_REL

source_name: pediatric AML sample 937


title: gDNA from relapse pediatric AML 955

description:
pediatric AML
PAWWEE_REL

source_name: pediatric AML sample 955


title: gDNA from relapse pediatric AML 940

description:
pediatric AML
PAVUBN_REL

source_name: pediatric AML sample 940


title: gDNA from relapse pediatric AML 951

description:
pediatric AML
PAWCBZ_REL

source_name: pediatric AML sample 951


title: gDNA from relapse pediatric AML 950

description:
pediatric AML
PAWHJI_REL

source_name: pediatric AML sample 950


title: gDNA from relapse pediatric AML 935

description:
pediatric AML
PAVTRM_REL

source_name: pediatric AML sample 935


title: gDNA from relapse pediatric AML 938

description:
pediatric AML
PAVRJP_REL

source_name: pediatric AML sample 938


title: gDNA from relapse pediatric AML 936

description:
pediatric AML
PAUZRT_REL

source_name: pediatric AML sample 936


title: gDNA from relapse pediatric AML 929

description:
pediatric AML
PAVDYE_REL

source_name: pediatric AML sample 929


title: gDNA from relapse pediatric AML 930

description:
pediatric AML
PAVNUW_REL

source_name: pediatric AML sample 930


title: gDNA from relapse pediatric AML 931

description:
pediatric AML
PAVTFI_REL

source_name: pediatric AML sample 931


title: gDNA from relapse pediatric AML 934

description:
pediatric AML
PAWCJK_REL

source_name: pediatric AML sample 934


title: gDNA from relapse pediatric AML 932

description:
pediatric AML
PAVSAN_REL

source_name: pediatric AML sample 932


title: gDNA from relapse pediatric AML 933

description:
pediatric AML
PAVTDU_REL

source_name: pediatric AML sample 933


title: gDNA from relapse pediatric AML 928

description:
pediatric AML
PAVPFR_REL

source_name: pediatric AML sample 928


title: gDNA from relapse pediatric AML 927

description:
pediatric AML
PAVDZK_REL

source_name: pediatric AML sample 927


title: gDNA from relapse pediatric AML 926

description:
pediatric AML
PAVALK_REL

source_name: pediatric AML sample 926


title: gDNA from relapse pediatric AML 946

description:
pediatric AML
PAWHFW_REL

source_name: pediatric AML sample 946


title: gDNA from relapse pediatric AML 944

description:
pediatric AML
PAWBSJ_REL

source_name: pediatric AML sample 944


title: gDNA from relapse pediatric AML 941

description:
pediatric AML
PAWAMB_REL

source_name: pediatric AML sample 941


title: gDNA from relapse pediatric AML 925

description:
pediatric AML
PAVHFP_REL

source_name: pediatric AML sample 925


title: gDNA from relapse pediatric AML 924

description:
pediatric AML
PAVJRF_REL

source_name: pediatric AML sample 924


title: gDNA from relapse pediatric AML 939

description:
pediatric AML
PAUUPR_REL

source_name: pediatric AML sample 939


title: gDNA from relapse pediatric AML 922

description:
pediatric AML
PAVPKA_REL

source_name: pediatric AML sample 922


title: gDNA from relapse pediatric AML 921

description:
pediatric AML
PAVLYV_REL

source_name: pediatric AML sample 921


title: gDNA from relapse pediatric AML 923

description:
pediatric AML
PAUYRR_REL

source_name: pediatric AML sample 923


title: gDNA from relapse pediatric AML 918

description:
pediatric AML
PAVBFN_REL

source_name: pediatric AML sample 918


title: gDNA from relapse pediatric AML 917

description:
pediatric AML
PAVHNV_REL

source_name: pediatric AML sample 917


title: gDNA from relapse pediatric AML 913

description:
pediatric AML
PAURJZ_REL

source_name: pediatric AML sample 913


title: gDNA from relapse pediatric AML 914

description:
pediatric AML
PAUJCF_REL

source_name: pediatric AML sample 914


title: gDNA from relapse pediatric AML 915

description:
pediatric AML
PAVLDU_REL

source_name: pediatric AML sample 915


title: gDNA from relapse pediatric AML 920

description:
pediatric AML
PAVKEX_REL

source_name: pediatric AML sample 920


title: gDNA from relapse pediatric AML 916

description:
pediatric AML
PAVDVV_REL

source_name: pediatric AML sample 916


title: gDNA from relapse pediatric AML 919

description:
pediatric AML
PAVGJG_REL

source_name: pediatric AML sample 919


title: gDNA from relapse pediatric AML 912

description:
pediatric AML
PAVDDA_REL

source_name: pediatric AML sample 912


title: gDNA from relapse pediatric AML 911

description:
pediatric AML
PAVCNG_REL

source_name: pediatric AML sample 911


title: gDNA from relapse pediatric AML 910

description:
pediatric AML
PAUPSX_REL

source_name: pediatric AML sample 910


title: gDNA from relapse pediatric AML 907

description:
pediatric AML
PAVEYP_REL

source_name: pediatric AML sample 907


title: gDNA from relapse pediatric AML 908

description:
pediatric AML
PAUZTH_REL

source_name: pediatric AML sample 908


title: gDNA from relapse pediatric AML 909

description:
pediatric AML
PAUYEV_REL

source_name: pediatric AML sample 909


title: gDNA from relapse pediatric AML 902

description:
pediatric AML
PAUVXT_REL

source_name: pediatric AML sample 902


title: gDNA from relapse pediatric AML 903

description:
pediatric AML
PAUMTZ_REL

source_name: pediatric AML sample 903


title: gDNA from relapse pediatric AML 901

description:
pediatric AML
PAURWH_REL

source_name: pediatric AML sample 901


title: gDNA from relapse pediatric AML 904

description:
pediatric AML
PAVBCV_REL

source_name: pediatric AML sample 904


title: gDNA from relapse pediatric AML 905

description:
pediatric AML
PAURUT_REL

source_name: pediatric AML sample 905


title: gDNA from relapse pediatric AML 899

description:
pediatric AML
PAVALI_REL

source_name: pediatric AML sample 899


title: gDNA from relapse pediatric AML 900

description:
pediatric AML
PAUNSV_REL

source_name: pediatric AML sample 900


title: gDNA from relapse pediatric AML 897

description:
pediatric AML
PAVGDM_REL

source_name: pediatric AML sample 897


title: gDNA from relapse pediatric AML 893

description:
pediatric AML
PAVLWV_REL

source_name: pediatric AML sample 893


title: gDNA from relapse pediatric AML 894

description:
pediatric AML
PAUVAT_REL

source_name: pediatric AML sample 894


title: gDNA from relapse pediatric AML 892

description:
pediatric AML
PAUUZT_REL

source_name: pediatric AML sample 892


title: gDNA from relapse pediatric AML 898

description:
pediatric AML
PAUSCS_REL

source_name: pediatric AML sample 898


title: gDNA from relapse pediatric AML 895

description:
pediatric AML
PAUVCB_REL

source_name: pediatric AML sample 895


title: gDNA from relapse pediatric AML 896

description:
pediatric AML
PAUVMN_REL

source_name: pediatric AML sample 896


title: gDNA from relapse pediatric AML 906

description:
pediatric AML
PAUVEF_REL

source_name: pediatric AML sample 906


title: gDNA from relapse pediatric AML 889

description:
pediatric AML
PAVRWU_REL

source_name: pediatric AML sample 889


title: gDNA from relapse pediatric AML 891

description:
pediatric AML
PAUXNM_REL

source_name: pediatric AML sample 891


title: gDNA from relapse pediatric AML 890

description:
pediatric AML
PAVGAM_REL

source_name: pediatric AML sample 890


title: gDNA from relapse pediatric AML 886

description:
pediatric AML
PAWUMM_REL

source_name: pediatric AML sample 886


title: gDNA from relapse pediatric AML 887

description:
pediatric AML
PAVLJH_REL

source_name: pediatric AML sample 887


title: gDNA from relapse pediatric AML 884

description:
pediatric AML
PAWENM_REL

source_name: pediatric AML sample 884


title: gDNA from relapse pediatric AML 883

description:
pediatric AML
PAWYJH_REL

source_name: pediatric AML sample 883


title: gDNA from relapse pediatric AML 882

description:
pediatric AML
PAWTNN_REL

source_name: pediatric AML sample 882


title: gDNA from relapse pediatric AML 880

description:
pediatric AML
PAWRVC_REL

source_name: pediatric AML sample 880


title: gDNA from relapse pediatric AML 879

description:
pediatric AML
PAWZAX_REL

source_name: pediatric AML sample 879


title: gDNA from relapse pediatric AML 878

description:
pediatric AML
PAWEKL_REL

source_name: pediatric AML sample 878


title: gDNA from relapse pediatric AML 877

description:
pediatric AML
PAWLKE_REL

source_name: pediatric AML sample 877


title: gDNA from relapse pediatric AML 875

description:
pediatric AML
PAUPIY_REL

source_name: pediatric AML sample 875


title: gDNA from relapse pediatric AML 881

description:
pediatric AML
PAWBSE_REL

source_name: pediatric AML sample 881


title: gDNA from relapse pediatric AML 885

description:
pediatric AML
PAWLUE_REL

source_name: pediatric AML sample 885


title: gDNA from relapse pediatric AML 873

description:
pediatric AML
PAWYZR_REL

source_name: pediatric AML sample 873


title: gDNA from relapse pediatric AML 876

description:
pediatric AML
PAXLEE_REL

source_name: pediatric AML sample 876


title: gDNA from relapse pediatric AML 874

description:
pediatric AML
PAWUUY_REL

source_name: pediatric AML sample 874


title: gDNA from relapse pediatric AML 872

description:
pediatric AML
PAXDXW_REL

source_name: pediatric AML sample 872


title: gDNA from relapse pediatric AML 871

description:
pediatric AML
PAXEPC_REL

source_name: pediatric AML sample 871


title: gDNA from relapse pediatric AML 870

description:
pediatric AML
PAXDHL_REL

source_name: pediatric AML sample 870


title: gDNA from relapse pediatric AML 869

description:
pediatric AML
PAXGDG_REL

source_name: pediatric AML sample 869


title: gDNA from relapse pediatric AML 868

description:
pediatric AML
PAXBAZ_REL

source_name: pediatric AML sample 868


title: gDNA from relapse pediatric AML 866

description:
pediatric AML
PAXMIJ_REL

source_name: pediatric AML sample 866


title: gDNA from relapse pediatric AML 867

description:
pediatric AML
PAXJGA_REL

source_name: pediatric AML sample 867


title: gDNA from relapse pediatric AML 863

description:
pediatric AML
PAWAMM_REL

source_name: pediatric AML sample 863


title: gDNA from relapse pediatric AML 865

description:
pediatric AML
PAWZAU_REL

source_name: pediatric AML sample 865


title: gDNA from relapse pediatric AML 864

description:
pediatric AML
PAWUNI_REL

source_name: pediatric AML sample 864


title: gDNA from relapse pediatric AML 862

description:
pediatric AML
PAVSVU_REL

source_name: pediatric AML sample 862


title: gDNA from relapse pediatric AML 861

description:
pediatric AML
PAWTYT_REL

source_name: pediatric AML sample 861


title: gDNA from relapse pediatric AML 860

description:
pediatric AML
PAWRPX_REL

source_name: pediatric AML sample 860


title: gDNA from relapse pediatric AML 855

description:
pediatric AML
PAWSJC_REL

source_name: pediatric AML sample 855


title: gDNA from relapse pediatric AML 888

description:
pediatric AML
PAVSFB_REL

source_name: pediatric AML sample 888


title: gDNA from relapse pediatric AML 856

description:
pediatric AML
PAXMLI_REL

source_name: pediatric AML sample 856


title: gDNA from diagnosic pediatric AML 854

description:
pediatric AML
PAXJGA_Dx

source_name: pediatric AML sample 854

value: Diagnosis


title: gDNA from diagnosic pediatric AML 853

description:
pediatric AML
PAXJFL_Dx

source_name: pediatric AML sample 853


title: gDNA from diagnosic pediatric AML 852

description:
pediatric AML
PAXJFS_Dx

source_name: pediatric AML sample 852


title: gDNA from relapse pediatric AML 858

description:
pediatric AML
PAXIKL_REL

source_name: pediatric AML sample 858


title: gDNA from diagnosic pediatric AML 851

description:
pediatric AML
PAXJAA_Dx

source_name: pediatric AML sample 851


title: gDNA from diagnosic pediatric AML 849

description:
pediatric AML
PAXISV_Dx

source_name: pediatric AML sample 849


title: gDNA from relapse pediatric AML 857

description:
pediatric AML
PAWLKP_REL

source_name: pediatric AML sample 857


title: gDNA from diagnosic pediatric AML 843

description:
pediatric AML
PAXIEP_Dx

source_name: pediatric AML sample 843


title: gDNA from diagnosic pediatric AML 846

description:
pediatric AML
PAXIKD_Dx

source_name: pediatric AML sample 846


title: gDNA from diagnosic pediatric AML 844

description:
pediatric AML
PAXIHA_Dx

source_name: pediatric AML sample 844


title: gDNA from diagnosic pediatric AML 848

description:
pediatric AML
PAXIPJ_Dx

source_name: pediatric AML sample 848


title: gDNA from diagnosic pediatric AML 842

description:
pediatric AML
PAXIFA_Dx

source_name: pediatric AML sample 842


title: gDNA from diagnosic pediatric AML 847

description:
pediatric AML
PAXIKL_Dx

source_name: pediatric AML sample 847


title: gDNA from diagnosic pediatric AML 845

description:
pediatric AML
PAXIJB_Dx

source_name: pediatric AML sample 845


title: gDNA from diagnosic pediatric AML 841

description:
pediatric AML
PAXIEG_Dx

source_name: pediatric AML sample 841


title: gDNA from diagnosic pediatric AML 839

description:
pediatric AML
PAXICE_Dx

source_name: pediatric AML sample 839


title: gDNA from diagnosic pediatric AML 840

description:
pediatric AML
PAXIDA_Dx

source_name: pediatric AML sample 840


title: gDNA from diagnosic pediatric AML 838

description:
pediatric AML
PAXHZL_Dx

source_name: pediatric AML sample 838


title: gDNA from diagnosic pediatric AML 837

description:
pediatric AML
PAXIAZ_Dx

source_name: pediatric AML sample 837


title: gDNA from relapse pediatric AML 859

description:
pediatric AML
PAVAFA_REL

source_name: pediatric AML sample 859


title: gDNA from diagnosic pediatric AML 834

description:
pediatric AML
PAXHYG_Dx

source_name: pediatric AML sample 834


title: gDNA from diagnosic pediatric AML 833

description:
pediatric AML
PAXHTS_Dx

source_name: pediatric AML sample 833


title: gDNA from diagnosic pediatric AML 836

description:
pediatric AML
PAXHZD_Dx

source_name: pediatric AML sample 836


title: gDNA from diagnosic pediatric AML 835

description:
pediatric AML
PAXHWI_Dx

source_name: pediatric AML sample 835


title: gDNA from diagnosic pediatric AML 832

description:
pediatric AML
PAXHPH_Dx

source_name: pediatric AML sample 832


title: gDNA from diagnosic pediatric AML 831

description:
pediatric AML
PAXHGR_Dx

source_name: pediatric AML sample 831


title: gDNA from diagnosic pediatric AML 850

description:
pediatric AML
PAXIWR_Dx

source_name: pediatric AML sample 850


title: gDNA from diagnosic pediatric AML 830

description:
pediatric AML
PAXHGG_Dx

source_name: pediatric AML sample 830


title: gDNA from diagnosic pediatric AML 829

description:
pediatric AML
PAXHDA_Dx

source_name: pediatric AML sample 829


title: gDNA from diagnosic pediatric AML 828

description:
pediatric AML
PAXHCC_Dx

source_name: pediatric AML sample 828


title: gDNA from diagnosic pediatric AML 823

description:
pediatric AML
PAXGVH_Dx

source_name: pediatric AML sample 823


title: gDNA from diagnosic pediatric AML 821

description:
pediatric AML
PAXGPF_Dx

source_name: pediatric AML sample 821


title: gDNA from diagnosic pediatric AML 822

description:
pediatric AML
PAXGTM_Dx

source_name: pediatric AML sample 822

value: MECOM


title: gDNA from diagnosic pediatric AML 818

description:
pediatric AML
PAXGRE_Dx

source_name: pediatric AML sample 818


title: gDNA from diagnosic pediatric AML 820

description:
pediatric AML
PAXGSJ_Dx

source_name: pediatric AML sample 820


title: gDNA from diagnosic pediatric AML 824

description:
pediatric AML
PAXGVS_Dx

source_name: pediatric AML sample 824


title: gDNA from diagnosic pediatric AML 817

description:
pediatric AML
PAXGPE_Dx

source_name: pediatric AML sample 817


title: gDNA from diagnosic pediatric AML 827

description:
pediatric AML
PAXGZB_Dx

source_name: pediatric AML sample 827


title: gDNA from diagnosic pediatric AML 815

description:
pediatric AML
PAXGKH_Dx

source_name: pediatric AML sample 815


title: gDNA from diagnosic pediatric AML 814

description:
pediatric AML
PAXGHE_Dx

source_name: pediatric AML sample 814


title: gDNA from diagnosic pediatric AML 816

description:
pediatric AML
PAXGNI_Dx

source_name: pediatric AML sample 816


title: gDNA from diagnosic pediatric AML 813

description:
pediatric AML
PAXGIX_Dx

source_name: pediatric AML sample 813


title: gDNA from diagnosic pediatric AML 811

description:
pediatric AML
PAXGGM_Dx

source_name: pediatric AML sample 811


title: gDNA from diagnosic pediatric AML 826

description:
pediatric AML
PAXGYZ_Dx

source_name: pediatric AML sample 826


title: gDNA from diagnosic pediatric AML 809

description:
pediatric AML
PAXGDZ_Dx

source_name: pediatric AML sample 809


title: gDNA from diagnosic pediatric AML 808

description:
pediatric AML
PAXGDG_Dx

source_name: pediatric AML sample 808


title: gDNA from diagnosic pediatric AML 803

description:
pediatric AML
PAXFIG_Dx

source_name: pediatric AML sample 803


title: gDNA from diagnosic pediatric AML 807

description:
pediatric AML
PAXFWY_Dx

source_name: pediatric AML sample 807


title: gDNA from diagnosic pediatric AML 801

description:
pediatric AML
PAXFEX_Dx

source_name: pediatric AML sample 801


title: gDNA from diagnosic pediatric AML 804

description:
pediatric AML
PAXFMH_Dx

source_name: pediatric AML sample 804


title: gDNA from diagnosic pediatric AML 806

description:
pediatric AML
PAXFSI_Dx

source_name: pediatric AML sample 806


title: gDNA from diagnosic pediatric AML 819

description:
pediatric AML
PAXGNZ_Dx

source_name: pediatric AML sample 819


title: gDNA from diagnosic pediatric AML 793

description:
pediatric AML
PAXEWG_Dx

source_name: pediatric AML sample 793


title: gDNA from diagnosic pediatric AML 799

description:
pediatric AML
PAXFEE_Dx

source_name: pediatric AML sample 799


title: gDNA from diagnosic pediatric AML 800

description:
pediatric AML
PAXFEA_Dx

source_name: pediatric AML sample 800


title: gDNA from diagnosic pediatric AML 795

description:
pediatric AML
PAXEWS_Dx

source_name: pediatric AML sample 795


title: gDNA from diagnosic pediatric AML 796

description:
pediatric AML
PAXETX_Dx

source_name: pediatric AML sample 796


title: gDNA from diagnosic pediatric AML 797

description:
pediatric AML
PAXFAG_Dx

source_name: pediatric AML sample 797


title: gDNA from diagnosic pediatric AML 794

description:
pediatric AML
PAXEWD_Dx

source_name: pediatric AML sample 794


title: gDNA from diagnosic pediatric AML 792

description:
pediatric AML
PAXETC_Dx

source_name: pediatric AML sample 792


title: gDNA from diagnosic pediatric AML 789

description:
pediatric AML
PAXEKE_Dx

source_name: pediatric AML sample 789


title: gDNA from diagnosic pediatric AML 798

description:
pediatric AML
PAXFBN_Dx

source_name: pediatric AML sample 798


title: gDNA from diagnosic pediatric AML 786

description:
pediatric AML
PAXEES_Dx

source_name: pediatric AML sample 786


title: gDNA from diagnosic pediatric AML 788

description:
pediatric AML
PAXEEY_Dx

source_name: pediatric AML sample 788


title: gDNA from diagnosic pediatric AML 790

description:
pediatric AML
PAXELP_Dx

source_name: pediatric AML sample 790


title: gDNA from diagnosic pediatric AML 791

description:
pediatric AML
PAXEPC_Dx

source_name: pediatric AML sample 791


title: gDNA from diagnosic pediatric AML 787

description:
pediatric AML
PAXEFX_Dx

source_name: pediatric AML sample 787


title: gDNA from diagnosic pediatric AML 812

description:
pediatric AML
PAXGIY_Dx

source_name: pediatric AML sample 812


title: gDNA from diagnosic pediatric AML 810

description:
pediatric AML
PAXGES_Dx

source_name: pediatric AML sample 810


title: gDNA from diagnosic pediatric AML 805

description:
pediatric AML
PAXFDN_Dx

source_name: pediatric AML sample 805


title: gDNA from diagnosic pediatric AML 785

description:
pediatric AML
PAXEBW_Dx

source_name: pediatric AML sample 785


title: gDNA from diagnosic pediatric AML 802

description:
pediatric AML
PAXFHW_Dx

source_name: pediatric AML sample 802


title: gDNA from diagnosic pediatric AML 777

description:
pediatric AML
PAXDEG_Dx

source_name: pediatric AML sample 777


title: gDNA from diagnosic pediatric AML 778

description:
pediatric AML
PAXDGH_Dx

source_name: pediatric AML sample 778


title: gDNA from diagnosic pediatric AML 779

description:
pediatric AML
PAXDHL_Dx

source_name: pediatric AML sample 779


title: gDNA from diagnosic pediatric AML 783

description:
pediatric AML
PAXDSN_Dx

source_name: pediatric AML sample 783


title: gDNA from diagnosic pediatric AML 782

description:
pediatric AML
PAXDNI_Dx

source_name: pediatric AML sample 782


title: gDNA from diagnosic pediatric AML 776

description:
pediatric AML
PAXDEX_Dx

source_name: pediatric AML sample 776


title: gDNA from diagnosic pediatric AML 780

description:
pediatric AML
PAXDMP_Dx

source_name: pediatric AML sample 780


title: gDNA from diagnosic pediatric AML 781

description:
pediatric AML
PAXDNA_Dx

source_name: pediatric AML sample 781


title: gDNA from diagnosic pediatric AML 784

description:
pediatric AML
PAXDXW_Dx

source_name: pediatric AML sample 784


title: gDNA from diagnosic pediatric AML 774

description:
pediatric AML
PAXDDY_Dx

source_name: pediatric AML sample 774


title: gDNA from diagnosic pediatric AML 772

description:
pediatric AML
PAXDBF_Dx

source_name: pediatric AML sample 772


title: gDNA from diagnosic pediatric AML 771

description:
pediatric AML
PAXCYN_Dx

source_name: pediatric AML sample 771


title: gDNA from diagnosic pediatric AML 767

description:
pediatric AML
PAXCVU_Dx

source_name: pediatric AML sample 767


title: gDNA from diagnosic pediatric AML 765

description:
pediatric AML
PAXCNV_Dx

source_name: pediatric AML sample 765


title: gDNA from diagnosic pediatric AML 775

description:
pediatric AML
PAXDEL_Dx

source_name: pediatric AML sample 775


title: gDNA from diagnosic pediatric AML 766

description:
pediatric AML
PAXCVR_Dx

source_name: pediatric AML sample 766


title: gDNA from diagnosic pediatric AML 763

description:
pediatric AML
PAXCLX_Dx

source_name: pediatric AML sample 763


title: gDNA from diagnosic pediatric AML 760

description:
pediatric AML
PAXCEV_Dx

source_name: pediatric AML sample 760


title: gDNA from diagnosic pediatric AML 761

description:
pediatric AML
PAXCCW_Dx

source_name: pediatric AML sample 761


title: gDNA from diagnosic pediatric AML 759

description:
pediatric AML
PAXCDU_Dx

source_name: pediatric AML sample 759


title: gDNA from diagnosic pediatric AML 757

description:
pediatric AML
PAXBXI_Dx

source_name: pediatric AML sample 757


title: gDNA from diagnosic pediatric AML 758

description:
pediatric AML
PAXBZH_Dx

source_name: pediatric AML sample 758


title: gDNA from diagnosic pediatric AML 756

description:
pediatric AML
PAXBVX_Dx

source_name: pediatric AML sample 756


title: gDNA from diagnosic pediatric AML 754

description:
pediatric AML
PAXBPF_Dx

source_name: pediatric AML sample 754


title: gDNA from diagnosic pediatric AML 755

description:
pediatric AML
PAXBSE_Dx

source_name: pediatric AML sample 755


title: gDNA from diagnosic pediatric AML 753

description:
pediatric AML
PAXBNE_Dx

source_name: pediatric AML sample 753


title: gDNA from diagnosic pediatric AML 769

description:
pediatric AML
PAXCWR_Dx

source_name: pediatric AML sample 769


title: gDNA from diagnosic pediatric AML 773

description:
pediatric AML
PAXCZX_Dx

source_name: pediatric AML sample 773


title: gDNA from diagnosic pediatric AML 762

description:
pediatric AML
PAXCLE_Dx

source_name: pediatric AML sample 762


title: gDNA from diagnosic pediatric AML 764

description:
pediatric AML
PAXCPM_Dx

source_name: pediatric AML sample 764


title: gDNA from diagnosic pediatric AML 752

description:
pediatric AML
PAXBLX_Dx

source_name: pediatric AML sample 752


title: gDNA from diagnosic pediatric AML 751

description:
pediatric AML
PAXBLW_Dx

source_name: pediatric AML sample 751


title: gDNA from diagnosic pediatric AML 770

description:
pediatric AML
PAXCYJ_Dx

source_name: pediatric AML sample 770


title: gDNA from diagnosic pediatric AML 749

description:
pediatric AML
PAXBHX_Dx

source_name: pediatric AML sample 749


title: gDNA from diagnosic pediatric AML 750

description:
pediatric AML
PAXBLJ_Dx

source_name: pediatric AML sample 750


title: gDNA from diagnosic pediatric AML 746

description:
pediatric AML
PAXBDM_Dx

source_name: pediatric AML sample 746


title: gDNA from diagnosic pediatric AML 825

description:
pediatric AML
PAXGXR_Dx

source_name: pediatric AML sample 825


title: gDNA from diagnosic pediatric AML 747

description:
pediatric AML
PAXBCW_Dx

source_name: pediatric AML sample 747


title: gDNA from diagnosic pediatric AML 742

description:
pediatric AML
PAXARX_Dx

source_name: pediatric AML sample 742


title: gDNA from diagnosic pediatric AML 743

description:
pediatric AML
PAXAXY_Dx

source_name: pediatric AML sample 743


title: gDNA from diagnosic pediatric AML 768

description:
pediatric AML
PAXCWZ_Dx

source_name: pediatric AML sample 768


title: gDNA from diagnosic pediatric AML 739

description:
pediatric AML
PAXALR_Dx

source_name: pediatric AML sample 739


title: gDNA from diagnosic pediatric AML 738

description:
pediatric AML
PAXAKF_Dx

source_name: pediatric AML sample 738


title: gDNA from diagnosic pediatric AML 736

description:
pediatric AML
PAXACP_Dx

source_name: pediatric AML sample 736


title: gDNA from diagnosic pediatric AML 745

description:
pediatric AML
PAXBAZ_Dx

source_name: pediatric AML sample 745


title: gDNA from diagnosic pediatric AML 735

description:
pediatric AML
PAXACY_Dx

source_name: pediatric AML sample 735


title: gDNA from diagnosic pediatric AML 737

description:
pediatric AML
PAXAFN_Dx

source_name: pediatric AML sample 737


title: gDNA from diagnosic pediatric AML 733

description:
pediatric AML
PAWZZS_Dx

source_name: pediatric AML sample 733


title: gDNA from diagnosic pediatric AML 731

description:
pediatric AML
PAWZZN_Dx

source_name: pediatric AML sample 731


title: gDNA from diagnosic pediatric AML 732

description:
pediatric AML
PAXAAA_Dx

source_name: pediatric AML sample 732


title: gDNA from diagnosic pediatric AML 744

description:
pediatric AML
PAXBAV_Dx

source_name: pediatric AML sample 744


title: gDNA from diagnosic pediatric AML 730

description:
pediatric AML
PAWZVT_Dx

source_name: pediatric AML sample 730


title: gDNA from diagnosic pediatric AML 729

description:
pediatric AML
PAWZWN_Dx

source_name: pediatric AML sample 729


title: gDNA from diagnosic pediatric AML 726

description:
pediatric AML
PAWZNG_Dx

source_name: pediatric AML sample 726


title: gDNA from diagnosic pediatric AML 728

description:
pediatric AML
PAWZUZ_Dx

source_name: pediatric AML sample 728


title: gDNA from diagnosic pediatric AML 725

description:
pediatric AML
PAWZKW_Dx

source_name: pediatric AML sample 725


title: gDNA from diagnosic pediatric AML 748

description:
pediatric AML
PAXBEF_Dx

source_name: pediatric AML sample 748


title: gDNA from diagnosic pediatric AML 721

description:
pediatric AML
PAWYZR_Dx

source_name: pediatric AML sample 721


title: gDNA from diagnosic pediatric AML 723

description:
pediatric AML
PAWZIG_Dx

source_name: pediatric AML sample 723


title: gDNA from diagnosic pediatric AML 727

description:
pediatric AML
PAWZUF_Dx

source_name: pediatric AML sample 727


title: gDNA from diagnosic pediatric AML 720

description:
pediatric AML
PAWZAU_Dx

source_name: pediatric AML sample 720


title: gDNA from diagnosic pediatric AML 718

description:
pediatric AML
PAWZAW_Dx

source_name: pediatric AML sample 718


title: gDNA from diagnosic pediatric AML 719

description:
pediatric AML
PAWZAX_Dx

source_name: pediatric AML sample 719


title: gDNA from diagnosic pediatric AML 724

description:
pediatric AML
PAWZIX_Dx

source_name: pediatric AML sample 724


title: gDNA from diagnosic pediatric AML 717

description:
pediatric AML
PAWYUC_Dx

source_name: pediatric AML sample 717


title: gDNA from diagnosic pediatric AML 713

description:
pediatric AML
PAWYNC_Dx

source_name: pediatric AML sample 713


title: gDNA from diagnosic pediatric AML 740

description:
pediatric AML
PAXANS_Dx

source_name: pediatric AML sample 740


title: gDNA from diagnosic pediatric AML 711

description:
pediatric AML
PAWYGY_Dx

source_name: pediatric AML sample 711


title: gDNA from diagnosic pediatric AML 710

description:
pediatric AML
PAWYJF_Dx

source_name: pediatric AML sample 710


title: gDNA from diagnosic pediatric AML 714

description:
pediatric AML
PAWYRT_Dx

source_name: pediatric AML sample 714


title: gDNA from diagnosic pediatric AML 734

description:
pediatric AML
PAXAFS_Dx

source_name: pediatric AML sample 734


title: gDNA from diagnosic pediatric AML 708

description:
pediatric AML
PAWYJH_Dx

source_name: pediatric AML sample 708


title: gDNA from diagnosic pediatric AML 706

description:
pediatric AML
PAWYEM_Dx

source_name: pediatric AML sample 706


title: gDNA from diagnosic pediatric AML 741

description:
pediatric AML
PAXARD_Dx

source_name: pediatric AML sample 741


title: gDNA from diagnosic pediatric AML 709

description:
pediatric AML
PAWYKA_Dx

source_name: pediatric AML sample 709


title: gDNA from diagnosic pediatric AML 705

description:
pediatric AML
PAWYEK_Dx

source_name: pediatric AML sample 705


title: gDNA from diagnosic pediatric AML 707

description:
pediatric AML
PAWYEP_Dx

source_name: pediatric AML sample 707


title: gDNA from diagnosic pediatric AML 704

description:
pediatric AML
PAWYDD_Dx

source_name: pediatric AML sample 704


title: gDNA from diagnosic pediatric AML 701

description:
pediatric AML
PAWXYG_Dx

source_name: pediatric AML sample 701


title: gDNA from diagnosic pediatric AML 716

description:
pediatric AML
PAWYVR_Dx

source_name: pediatric AML sample 716


title: gDNA from diagnosic pediatric AML 703

description:
pediatric AML
PAWXWC_Dx

source_name: pediatric AML sample 703


title: gDNA from diagnosic pediatric AML 696

description:
pediatric AML
PAWXCM_Dx

source_name: pediatric AML sample 696


title: gDNA from diagnosic pediatric AML 699

description:
pediatric AML
PAWXSL_Dx

source_name: pediatric AML sample 699


title: gDNA from diagnosic pediatric AML 697

description:
pediatric AML
PAWWZL_Dx

source_name: pediatric AML sample 697


title: gDNA from diagnosic pediatric AML 702

description:
pediatric AML
PAWXZJ_Dx

source_name: pediatric AML sample 702


title: gDNA from diagnosic pediatric AML 698

description:
pediatric AML
PAWXIA_Dx

source_name: pediatric AML sample 698