title: SMM patient 28

source_name: RNA - CD138-depleted bone marrow cells

value: SMM


title: SMM patient 27

status: Public on Dec 15 2021

type: RNA

city: Barcelona

first: Ester

last: Lozano

state: Barcelona

address: Rosselló, 153

department: Hemato-Oncology

country: Spain

institute: IDIBAPS

hyb_protocol: A minimum of 100 ng of total RNA per sample was loaded and run on the HuV1_Cancer Immu_v1_1_Nanostring for analysis of the NanoString PanCancer Immune Profiling Panel

scan_protocol: The sample cartridge was scanned by an nCounter Digital Analyse (NanoString Technologies) at 555 fields of view.

data_processing: The raw data were re-scaled to account for the differences in raw code counts. This was performed using nSolver Analysis Software (NanoString Technologies), incorporating positive, negative and 'normalisation' gene target counts.

molecule: total RNA

organism: Homo sapiens

label_protocol: Capture probes and reporter probes (NanoString Technologies) were added to the extracted 100ng of mRNA according to manufacturer guidelines.

extract_protocol: CD138-depleted BM cell fraction was isolated with anti-CD138 mAb-coated immunomagnetic beads using an AutoMacs cell sorter (Milteny Biotec, Bergisch Gladbach, Germany). Total RNA from the CD138neg BM cell fraction was extracted using the TRIzol reagent (Thermo Fisher Scientific, Waltham, MA) according to manufacturer’s instructions.

tag: disease


title: gDNA from diagnosic pediatric AML 213

type: genomic

city: Seattle

first: Soheil

last: Meshinchi

state: Washington

address: 1100 Fairview Ave N.

department: Clinical Research Division

country: USA

institute: Fred Hutchinson Cancer Research Center

description:
pediatric AML
PAVIDJ_Dx

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

molecule: genomic DNA

source_name: pediatric AML sample 213

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

tag: Sex

value: Male

tag: age (years)

tag: timepoint

value: Diagnosis

tag: fusion


title: gDNA from diagnosic pediatric AML 227

description:
pediatric AML
PAVKAU_Dx

source_name: pediatric AML sample 227

value: Female


title: gDNA from diagnosic pediatric AML 210

description:
pediatric AML
PAVHUI_Dx

source_name: pediatric AML sample 210


title: gDNA from diagnosic pediatric AML 211

description:
pediatric AML
PAVHWK_Dx

source_name: pediatric AML sample 211


title: SMM patient 26


title: SMM patient 25


title: gDNA from diagnosic pediatric AML 220

description:
pediatric AML
PAVJCJ_Dx

source_name: pediatric AML sample 220


title: SMM patient 24


title: SMM patient 23


title: SMM patient 22


title: gDNA from diagnosic pediatric AML 207

description:
pediatric AML
PAVHNV_Dx

source_name: pediatric AML sample 207


title: gDNA from diagnosic pediatric AML 206

description:
pediatric AML
PAVHML_Dx

source_name: pediatric AML sample 206


title: gDNA from diagnosic pediatric AML 208

description:
pediatric AML
PAVHTL_Dx

source_name: pediatric AML sample 208


title: gDNA from diagnosic pediatric AML 217

description:
pediatric AML
PAVINA_Dx

source_name: pediatric AML sample 217


title: gDNA from diagnosic pediatric AML 203

description:
pediatric AML
PAVHCV_Dx

source_name: pediatric AML sample 203


title: gDNA from diagnosic pediatric AML 202

description:
pediatric AML
PAVGYA_Dx

source_name: pediatric AML sample 202


title: gDNA from diagnosic pediatric AML 201

description:
pediatric AML
PAVGXF_Dx

source_name: pediatric AML sample 201


title: gDNA from diagnosic pediatric AML 198

description:
pediatric AML
PAVGNC_Dx

source_name: pediatric AML sample 198


title: SMM patient 20


title: gDNA from diagnosic pediatric AML 212

description:
pediatric AML
PAVIDD_Dx

source_name: pediatric AML sample 212


title: gDNA from diagnosic pediatric AML 200

description:
pediatric AML
PAVGXC_Dx

source_name: pediatric AML sample 200


title: gDNA from diagnosic pediatric AML 197

description:
pediatric AML
PAVGIX_Dx

source_name: pediatric AML sample 197


title: gDNA from diagnosic pediatric AML 196

description:
pediatric AML
PAVGIV_Dx

source_name: pediatric AML sample 196


title: SMM patient 18

source_name: RNA - CD138-depleted bone marrow cells


title: gDNA from diagnosic pediatric AML 209

description:
pediatric AML
PAVHUF_Dx

source_name: pediatric AML sample 209


title: SMM patient 17


title: gDNA from diagnosic pediatric AML 195

description:
pediatric AML
PAVGKS_Dx

source_name: pediatric AML sample 195


title: gDNA from diagnosic pediatric AML 194

description:
pediatric AML
PAVGJG_Dx

source_name: pediatric AML sample 194


title: gDNA from diagnosic pediatric AML 205

description:
pediatric AML
PAVHLI_Dx

source_name: pediatric AML sample 205


title: gDNA from diagnosic pediatric AML 204

description:
pediatric AML
PAVHFP_Dx

source_name: pediatric AML sample 204


title: gDNA from diagnosic pediatric AML 192

description:
pediatric AML
PAVGDM_Dx

source_name: pediatric AML sample 192


title: gDNA from diagnosic pediatric AML 193

description:
pediatric AML
PAVGEV_Dx

source_name: pediatric AML sample 193


title: SMM patient 16


title: gDNA from diagnosic pediatric AML 191

description:
pediatric AML
PAVGBH_Dx

source_name: pediatric AML sample 191


title: gDNA from diagnosic pediatric AML 190

description:
pediatric AML
PAVGAM_Dx

source_name: pediatric AML sample 190


title: gDNA from diagnosic pediatric AML 189

description:
pediatric AML
PAVFWI_Dx

source_name: pediatric AML sample 189


title: SMM patient 15


title: SMM patient 14


title: SMM patient 21


title: gDNA from diagnosic pediatric AML 199

description:
pediatric AML
PAVGUM_Dx

source_name: pediatric AML sample 199


title: SMM patient 19


title: SMM patient 13


title: gDNA from diagnosic pediatric AML 188

description:
pediatric AML
PAVFPR_Dx

source_name: pediatric AML sample 188


title: gDNA from diagnosic pediatric AML 187

description:
pediatric AML
PAVFDW_Dx

source_name: pediatric AML sample 187


title: gDNA from diagnosic pediatric AML 186

description:
pediatric AML
PAVFEM_Dx

source_name: pediatric AML sample 186


title: gDNA from diagnosic pediatric AML 184

description:
pediatric AML
PAVEYP_Dx

source_name: pediatric AML sample 184


title: gDNA from diagnosic pediatric AML 183

description:
pediatric AML
PAVENG_Dx

source_name: pediatric AML sample 183


title: gDNA from diagnosic pediatric AML 182

description:
pediatric AML
PAVEMX_Dx

source_name: pediatric AML sample 182


title: SMM patient 12

source_name: RNA - CD138-depleted bone marrow cells


title: SMM patient 11


title: gDNA from diagnosic pediatric AML 181

description:
pediatric AML
PAVELC_Dx

source_name: pediatric AML sample 181


title: gDNA from diagnosic pediatric AML 290

description:
pediatric AML
PAVPDN_Dx

source_name: pediatric AML sample 290


title: GBM Patient [rGBM-03-2]

type: SRA

city: Farmington

first: Parveen

last: Kumar

state: Connecticut

address: 10 Farmington Drive

institute: Application Computational Scientist

library_source: transcriptomic

data_processing:
FASTQ files were generated and demultiplexed using Illumina bcl2fastq 2.18.0.12.
For Patient rGBM-01 and ndGBM-01, the sequencing was performed on Illumina for 150 cycles with sequencing recommended condition (Read1: 26nt, Read2: 98nt and Index1: 8 nt). For the remaining patients, the sequencing was performed on Illumina for 300 cycles with sequencing recommended condition (Read1: 151nt, Read2: 151nt and Index1: 8 nt).
Raw FASTQ reads from Illumina were aligned to GRCh38 (human) using CellRanger V5 software from 10X Genomics with default parameters. As an output, Cellranger also generates a bam for each sample
Genome_build: GRCh38 (human)
Supplementary_files_format_and_content: Counts matrices are in Matrix Market CSR format and gzipped.  Rows correspond to genes in the associated genes.tsv.gz and columns correspond to cell-barcodes in associated barcodes.tsv.gz

molecule: polyA RNA

source_name: Human Tumor Tissue

growth_protocol: fresh tumors tissues were obtained from patients

extract_protocol:
Fresh tumor tissues were dissociated and captured using 10X Genomics Chromium system following the 10X Genomics 3' Transcriptomics kit V1
Following 10X Genomics 3' Transcriptomics kit V1, Sequenced at BGI using DNBseq.

tag: subject status

value: GBM Patient

tag: tumor grade

value: IV


title: SMM patient 10


title: gDNA from diagnosic pediatric AML 178

description:
pediatric AML
PAVEAF_Dx

source_name: pediatric AML sample 178


title: SMM patient 9


title: gDNA from diagnosic pediatric AML 180

description:
pediatric AML
PAVELT_Dx

source_name: pediatric AML sample 180


title: gDNA from diagnosic pediatric AML 176

description:
pediatric AML
PAVDZK_Dx

source_name: pediatric AML sample 176


title: gDNA from diagnosic pediatric AML 177

description:
pediatric AML
PAVDZL_Dx

source_name: pediatric AML sample 177


title: gDNA from diagnosic pediatric AML 179

description:
pediatric AML
PAVEEI_Dx

source_name: pediatric AML sample 179


title: MGUS patient 22

value: MGUS


title: MGUS patient 21


title: gDNA from diagnosic pediatric AML 173

description:
pediatric AML
PAVDXS_Dx

source_name: pediatric AML sample 173


title: MGUS patient 20


title: gDNA from diagnosic pediatric AML 170

description:
pediatric AML
PAVDNF_Dx

source_name: pediatric AML sample 170


title: gDNA from diagnosic pediatric AML 171

description:
pediatric AML
PAVDVV_Dx

source_name: pediatric AML sample 171


title: gDNA from diagnosic pediatric AML 169

description:
pediatric AML
PAVDRG_Dx

source_name: pediatric AML sample 169


title: gDNA from diagnosic pediatric AML 172

description:
pediatric AML
PAVDVU_Dx

source_name: pediatric AML sample 172


title: gDNA from diagnosic pediatric AML 185

description:
pediatric AML
PAVEZN_Dx

source_name: pediatric AML sample 185


title: gDNA from diagnosic pediatric AML 168

description:
pediatric AML
PAVDPF_Dx

source_name: pediatric AML sample 168


title: MGUS patient 18


title: MGUS patient 17


title: gDNA from diagnosic pediatric AML 167

description:
pediatric AML
PAVDHJ_Dx

source_name: pediatric AML sample 167


title: gDNA from diagnosic pediatric AML 166

description:
pediatric AML
PAVDGM_Dx

source_name: pediatric AML sample 166


title: MGUS patient 16

source_name: RNA - CD138-depleted bone marrow cells


title: gDNA from diagnosic pediatric AML 163

description:
pediatric AML
PAVDDA_Dx

source_name: pediatric AML sample 163


title: gDNA from diagnosic pediatric AML 165

description:
pediatric AML
PAVDGR_Dx

source_name: pediatric AML sample 165


title: MGUS patient 19


title: gDNA from diagnosic pediatric AML 164

description:
pediatric AML
PAVDFC_Dx

source_name: pediatric AML sample 164


title: gDNA from diagnosic pediatric AML 162

description:
pediatric AML
PAVDBT_Dx

source_name: pediatric AML sample 162


title: gDNA from diagnosic pediatric AML 161

description:
pediatric AML
PAVDBK_Dx

source_name: pediatric AML sample 161


title: gDNA from diagnosic pediatric AML 175

description:
pediatric AML
PAVDZI_Dx

source_name: pediatric AML sample 175


title: MGUS patient 14


title: MGUS patient 15


title: gDNA from diagnosic pediatric AML 159

description:
pediatric AML
PAVDAB_Dx

source_name: pediatric AML sample 159


title: gDNA from diagnosic pediatric AML 160

description:
pediatric AML
PAVDAJ_Dx

source_name: pediatric AML sample 160


title: gDNA from diagnosic pediatric AML 158

description:
pediatric AML
PAVCZF_Dx

source_name: pediatric AML sample 158


title: gDNA from diagnosic pediatric AML 157

description:
pediatric AML
PAVCVD_Dx

source_name: pediatric AML sample 157


title: gDNA from diagnosic pediatric AML 156

description:
pediatric AML
PAVCWT_Dx

source_name: pediatric AML sample 156


title: gDNA from diagnosic pediatric AML 174

description:
pediatric AML
PAVDYE_Dx

source_name: pediatric AML sample 174


title: MGUS patient 13


title: MGUS patient 12


title: gDNA from diagnosic pediatric AML 152

description:
pediatric AML
PAVCMR_Dx

source_name: pediatric AML sample 152


title: gDNA from diagnosic pediatric AML 153

description:
pediatric AML
PAVCNG_Dx

source_name: pediatric AML sample 153


title: MGUS patient 11


title: MGUS patient 10


title: gDNA from diagnosic pediatric AML 151

description:
pediatric AML
PAVCNU_Dx

source_name: pediatric AML sample 151


title: gDNA from diagnosic pediatric AML 150

description:
pediatric AML
PAVCJB_Dx

source_name: pediatric AML sample 150


title: gDNA from diagnosic pediatric AML 154

description:
pediatric AML
PAVCRM_Dx

source_name: pediatric AML sample 154


title: MGUS patient 9

source_name: RNA - CD138-depleted bone marrow cells


title: gDNA from diagnosic pediatric AML 148

description:
pediatric AML
PAVCFR_Dx

source_name: pediatric AML sample 148


title: gDNA from diagnosic pediatric AML 149

description:
pediatric AML
PAVCHU_Dx

source_name: pediatric AML sample 149


title: MM patient 8

description: RNA was extracted using Trizol reagent as per manufacturer's specifications

extract_protocol: Capture probes and reporter probes (NanoString Technologies) were added to the extracted 100ng of mRNA according to manufacturer guidelines.

value: MM


title: gDNA from diagnosic pediatric AML 147

description:
pediatric AML
PAVBZM_Dx

source_name: pediatric AML sample 147


title: gDNA from diagnosic pediatric AML 146

description:
pediatric AML
PAVBZY_Dx

source_name: pediatric AML sample 146


title: MM patient 6


title: gDNA from diagnosic pediatric AML 145

description:
pediatric AML
PAVBWL_Dx

source_name: pediatric AML sample 145


title: gDNA from diagnosic pediatric AML 155

description:
pediatric AML
PAVCPM_Dx

source_name: pediatric AML sample 155


title: gDNA from diagnosic pediatric AML 140

description:
pediatric AML
PAVBIY_Dx

source_name: pediatric AML sample 140


title: MM patient 5


title: gDNA from diagnosic pediatric AML 136

description:
pediatric AML
PAVBCV_Dx

source_name: pediatric AML sample 136


title: gDNA from diagnosic pediatric AML 144

description:
pediatric AML
PAVBUX_Dx

source_name: pediatric AML sample 144


title: MM patient 7


title: gDNA from diagnosic pediatric AML 133

description:
pediatric AML
PAVAYH_Dx

source_name: pediatric AML sample 133


title: MM patient 2


title: gDNA from diagnosic pediatric AML 143

description:
pediatric AML
PAVBVA_Dx

source_name: pediatric AML sample 143


title: gDNA from diagnosic pediatric AML 132

description:
pediatric AML
PAVAWS_Dx

source_name: pediatric AML sample 132


title: gDNA from diagnosic pediatric AML 142

description:
pediatric AML
PAVBNV_Dx

source_name: pediatric AML sample 142


title: SMM patient 8


title: MM patient 4


title: gDNA from diagnosic pediatric AML 130

description:
pediatric AML
PAVAFA_Dx

source_name: pediatric AML sample 130


title: gDNA from diagnosic pediatric AML 131

description:
pediatric AML
PAVAVV_Dx

source_name: pediatric AML sample 131


title: gDNA from diagnosic pediatric AML 141

description:
pediatric AML
PAVBMM_Dx

source_name: pediatric AML sample 141


title: MM patient 3

source_name: RNA - CD138-depleted bone marrow cells


title: gDNA from diagnosic pediatric AML 139

description:
pediatric AML
PAVBIH_Dx

source_name: pediatric AML sample 139


title: gDNA from diagnosic pediatric AML 137

description:
pediatric AML
PAVBFN_Dx

source_name: pediatric AML sample 137


title: gDNA from diagnosic pediatric AML 138

description:
pediatric AML
PAVBEM_Dx

source_name: pediatric AML sample 138


title: gDNA from diagnosic pediatric AML 135

description:
pediatric AML
PAVBAY_Dx

source_name: pediatric AML sample 135


title: gDNA from diagnosic pediatric AML 126

description:
pediatric AML
PAVALI_Dx

source_name: pediatric AML sample 126


title: gDNA from diagnosic pediatric AML 134

description:
pediatric AML
PAVAYD_Dx

source_name: pediatric AML sample 134


title: MM patient 1


title: SMM patient 7


title: gDNA from diagnosic pediatric AML 125

description:
pediatric AML
PAVALK_Dx

source_name: pediatric AML sample 125


title: gDNA from diagnosic pediatric AML 128

description:
pediatric AML
PAVANT_Dx

source_name: pediatric AML sample 128


title: gDNA from diagnosic pediatric AML 129

description:
pediatric AML
PAVANX_Dx

source_name: pediatric AML sample 129


title: SMM patient 3


title: gDNA from diagnosic pediatric AML 122

description:
pediatric AML
PAVAFJ_Dx

source_name: pediatric AML sample 122


title: gDNA from diagnosic pediatric AML 123

description:
pediatric AML
PAVAGA_Dx

source_name: pediatric AML sample 123


title: SMM patient 5


title: SMM patient 2


title: gDNA from diagnosic pediatric AML 121

description:
pediatric AML
PAVACZ_Dx

source_name: pediatric AML sample 121


title: SMM patient 1


title: SMM patient 4


title: gDNA from diagnosic pediatric AML 119

description:
pediatric AML
PAUZVW_Dx

source_name: pediatric AML sample 119


title: gDNA from diagnosic pediatric AML 127

description:
pediatric AML
PAVANE_Dx

source_name: pediatric AML sample 127


title: gDNA from diagnosic pediatric AML 124

description:
pediatric AML
PAVAKA_Dx

source_name: pediatric AML sample 124


title: MGUS patient 8


title: gDNA from diagnosic pediatric AML 118

description:
pediatric AML
PAUZVP_Dx

source_name: pediatric AML sample 118


title: SMM patient 6

source_name: RNA - CD138-depleted bone marrow cells


title: gDNA from diagnosic pediatric AML 116

description:
pediatric AML
PAUZRX_Dx

source_name: pediatric AML sample 116


title: gDNA from diagnosic pediatric AML 115

description:
pediatric AML
PAUZTH_Dx

source_name: pediatric AML sample 115


title: gDNA from diagnosic pediatric AML 117

description:
pediatric AML
PAUZTM_Dx

source_name: pediatric AML sample 117


title: MGUS patient 7


title: gDNA from diagnosic pediatric AML 114

description:
pediatric AML
PAUZRY_Dx

source_name: pediatric AML sample 114


title: gDNA from diagnosic pediatric AML 113

description:
pediatric AML
PAUZRT_Dx

source_name: pediatric AML sample 113


title: gDNA from diagnosic pediatric AML 112

description:
pediatric AML
PAUZPD_Dx

source_name: pediatric AML sample 112


title: MGUS patient 5


title: MGUS patient 4


title: gDNA from diagnosic pediatric AML 109

description:
pediatric AML
PAUYSN_Dx

source_name: pediatric AML sample 109


title: gDNA from diagnosic pediatric AML 110

description:
pediatric AML
PAUZJJ_Dx

source_name: pediatric AML sample 110


title: gDNA from diagnosic pediatric AML 111

description:
pediatric AML
PAUZMH_Dx

source_name: pediatric AML sample 111


title: gDNA from diagnosic pediatric AML 108

description:
pediatric AML
PAUZAM_Dx

source_name: pediatric AML sample 108


title: gDNA from diagnosic pediatric AML 106

description:
pediatric AML
PAUYUH_Dx

source_name: pediatric AML sample 106


title: gDNA from diagnosic pediatric AML 120

description:
pediatric AML
PAUYKH_Dx

source_name: pediatric AML sample 120


title: MGUS patient 3


title: gDNA from diagnosic pediatric AML 104

description:
pediatric AML
PAUYHR_Dx

source_name: pediatric AML sample 104


title: gDNA from diagnosic pediatric AML 105

description:
pediatric AML
PAUYRR_Dx

source_name: pediatric AML sample 105


title: MGUS patient 2


title: gDNA from diagnosic pediatric AML 103

description:
pediatric AML
PAUYEV_Dx

source_name: pediatric AML sample 103


title: gDNA from diagnosic pediatric AML 101

description:
pediatric AML
PAUYCA_Dx

source_name: pediatric AML sample 101


title: gDNA from diagnosic pediatric AML 100

description:
pediatric AML
PAUYAE_Dx

source_name: pediatric AML sample 100


title: MGUS patient 1

source_name: RNA - CD138-depleted bone marrow cells


title: gDNA from diagnosic pediatric AML 99

description:
pediatric AML
PAUXYG_Dx

source_name: pediatric AML sample 99


title: gDNA from diagnosic pediatric AML 102

description:
pediatric AML
PAUYDT_Dx

source_name: pediatric AML sample 102


title: WT_60_R6

city: Copenhagen

first: Axel

last: Thieffry

state: Hovedstaden

address: Lersø Parkallé 42-44

department: R&D

country: Denmark

institute: BioPhero-FMC

data_processing:
Basecalling with Illumina Cassava 1.8
Cutadapt v1.18+52 was used to remove the adapters
Clean reads were mapped on the TAIR10 referennce genome using HISAT2, keeping only concordant paired alignments
SAM alignment files were converted into BAM, then wig and finally bigWig with normalization in CPM (counts per millions)
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files (unstranded data), normalized into CPM (counts per millions)

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Following 12 days of growth in MS 1% under sterile conditions at room temperature and long-days luminosity, seedlings were transferred to liquid MS media 1% and allowed to acclimate 48 hours at 130 rpm prior to treatment.

extract_protocol:
A pool of 10 intact whole seedlings was flash frozen and total RNA was extracted using TRI-Reagent. Polysaccharide precipitation was carried out using the double sodium acetate method.
made by Novogene; Paired-end 150bp unstranded

treatment_protocol: flg22 peptide dissolved in DMSO (1 mg/mL) was added to the liquid MS for a final concentration of 3.3 uM. Treatment was conducted for three timepoints: 10 (not all samples), 30 and 60 minutes.

tag: tissue

value: whole seedlings

tag: background ecotype

tag: genotype

tag: age

value: 14 day-old

tag: mutation type

value: wild type

value: batch 1


title: gDNA from diagnosic pediatric AML 98

description:
pediatric AML
PAUXUA_Dx

source_name: pediatric AML sample 98


title: MGUS patient 6


title: gDNA from diagnosic pediatric AML 96

description:
pediatric AML
PAUXKI_Dx

source_name: pediatric AML sample 96


title: WT_60_R4


title: gDNA from diagnosic pediatric AML 94

description:
pediatric AML
PAUWYZ_Dx

source_name: pediatric AML sample 94


title: WT_60_R5


title: gDNA from diagnosic pediatric AML 107

description:
pediatric AML
PAUYWJ_Dx

source_name: pediatric AML sample 107


title: gDNA from diagnosic pediatric AML 95

description:
pediatric AML
PAUWYG_Dx

source_name: pediatric AML sample 95


title: WT_60_R3


title: gDNA from diagnosic pediatric AML 92

description:
pediatric AML
PAUWKY_Dx

source_name: pediatric AML sample 92


title: gDNA from diagnosic pediatric AML 90

description:
pediatric AML
PAUWRZ_Dx

source_name: pediatric AML sample 90


title: gDNA from diagnosic pediatric AML 89

description:
pediatric AML
PAUWHF_Dx

source_name: pediatric AML sample 89


title: gDNA from diagnosic pediatric AML 91

description:
pediatric AML
PAUWUZ_Dx

source_name: pediatric AML sample 91


title: WT_30_R6


title: WT_30_R5


title: gDNA from diagnosic pediatric AML 86

description:
pediatric AML
PAUWCF_Dx

source_name: pediatric AML sample 86


title: gDNA from diagnosic pediatric AML 87

description:
pediatric AML
PAUWEW_Dx

source_name: pediatric AML sample 87


title: gDNA from diagnosic pediatric AML 85

description:
pediatric AML
PAUVZD_Dx

source_name: pediatric AML sample 85


title: WT_30_R3


title: gDNA from diagnosic pediatric AML 81

description:
pediatric AML
PAUVPP_Dx

source_name: pediatric AML sample 81


title: WT_30_R4


title: gDNA from diagnosic pediatric AML 78

description:
pediatric AML
PAUVIB_Dx

source_name: pediatric AML sample 78


title: gDNA from diagnosic pediatric AML 79

description:
pediatric AML
PAUVCB_Dx

source_name: pediatric AML sample 79


title: gDNA from diagnosic pediatric AML 82

description:
pediatric AML
PAUVWV_Dx

source_name: pediatric AML sample 82


title: gDNA from diagnosic pediatric AML 80

description:
pediatric AML
PAUVMN_Dx

source_name: pediatric AML sample 80


title: gDNA from diagnosic pediatric AML 76

description:
pediatric AML
PAUVEF_Dx

source_name: pediatric AML sample 76


title: gDNA from diagnosic pediatric AML 84

description:
pediatric AML
PAUVXT_Dx

source_name: pediatric AML sample 84


title: gDNA from diagnosic pediatric AML 97

description:
pediatric AML
PAUXNH_Dx

source_name: pediatric AML sample 97


title: WT_10_R3

source_name: whole seedlings


title: WT_60_R2


title: gDNA from diagnosic pediatric AML 83

description:
pediatric AML
PAUVXU_Dx

source_name: pediatric AML sample 83


title: WT_30_R2


title: gDNA from diagnosic pediatric AML 75

description:
pediatric AML
PAUVBS_Dx

source_name: pediatric AML sample 75


title: gDNA from diagnosic pediatric AML 88

description:
pediatric AML
PAUWFM_Dx

source_name: pediatric AML sample 88


title: WT_30_R1


title: gDNA from diagnosic pediatric AML 93

description:
pediatric AML
PAUWYR_Dx

source_name: pediatric AML sample 93


title: gDNA from diagnosic pediatric AML 73

description:
pediatric AML
PAUVCL_Dx

source_name: pediatric AML sample 73


title: WT_10_R1


title: gDNA from diagnosic pediatric AML 71

description:
pediatric AML
PAUUZT_Dx

source_name: pediatric AML sample 71


title: gDNA from diagnosic pediatric AML 74

description:
pediatric AML
PAUVBZ_Dx

source_name: pediatric AML sample 74


title: gDNA from diagnosic pediatric AML 70

description:
pediatric AML
PAUUYJ_Dx

source_name: pediatric AML sample 70


title: gDNA from diagnosic pediatric AML 72

description:
pediatric AML
PAUVAT_Dx

source_name: pediatric AML sample 72


title: WT_10_R2


title: gDNA from diagnosic pediatric AML 67

description:
pediatric AML
PAUUPR_Dx

source_name: pediatric AML sample 67


title: gDNA from diagnosic pediatric AML 69

description:
pediatric AML
PAUUXA_Dx

source_name: pediatric AML sample 69


title: WT_0_R3


title: gDNA from diagnosic pediatric AML 68

description:
pediatric AML
PAUUTI_Dx

source_name: pediatric AML sample 68


title: gDNA from diagnosic pediatric AML 77

description:
pediatric AML
PAUVGD_Dx

source_name: pediatric AML sample 77


title: gDNA from diagnosic pediatric AML 64

description:
pediatric AML
PAUUKZ_Dx

source_name: pediatric AML sample 64


title: gDNA from diagnosic pediatric AML 61

description:
pediatric AML
PAUUCG_Dx

source_name: pediatric AML sample 61


title: gDNA from diagnosic pediatric AML 66

description:
pediatric AML
PAUURD_Dx

source_name: pediatric AML sample 66


title: WT_0_R1

source_name: whole seedlings


title: 102_Muscle

city: Fort Collins

first: Henry

middle: J

last: Thompson

state: CO

address: 1173 Campus Delivery

institute: Colorado State University

data_processing:
Illumina Real-Time Analysis (RTA) software version 3.4.4 was used for
fastp version 0.20.0 used for sequence trimming and quality control
hisat2 version 2.1.0 used for genome alignment mapped to rnor6 using Ensembl IDs
featureCounts version 1.6.4 used for tabulating the number of reads per gene
Genome_build: rnor6
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Muscle LIAC

extract_protocol:
Mammary tumor, mammary gland (MG) and muscle were harvested and snap frozen in liquid nitrogen. RNA was isolated from MG and muscle using Qiazol reagent and RNeasy mini kit (Qiagen, Inc., USA). Mammary tumor RNA was isloated using the RNeasy mini-kit (Qiagen, Inc.) with addition of a proteinase K digestion step for 10 min at 55 °C between the lysis buffer and ethanol steps.
RNA libraries were prepared for sequencing using standard Illumina protocols (Nugen Universal mRNA kit, Tecan Genomics, Inc., Redwood City, CA, USA)

tag: strain

value: Low Inherent Aerobic Capacity (LIAC)

value: muscle

tag: gender

value: female


title: 100_Muscle


title: gDNA from diagnosic pediatric AML 59

description:
pediatric AML
PAUTVU_Dx

source_name: pediatric AML sample 59


title: gDNA from diagnosic pediatric AML 65

description:
pediatric AML
PAUUMZ_Dx

source_name: pediatric AML sample 65


title: 99_Muscle


title: gDNA from diagnosic pediatric AML 63

description:
pediatric AML
PAUUKK_Dx

source_name: pediatric AML sample 63


title: gDNA from diagnosic pediatric AML 56

description:
pediatric AML
PAUSZL_Dx

source_name: pediatric AML sample 56


title: WT_60_R1


title: 104_Muscle


title: gDNA from diagnosic pediatric AML 60

description:
pediatric AML
PAUTWE_Dx

source_name: pediatric AML sample 60


title: 103_Muscle


title: gDNA from diagnosic pediatric AML 58

description:
pediatric AML
PAUTJD_Dx

source_name: pediatric AML sample 58


title: gDNA from diagnosic pediatric AML 50

description:
pediatric AML
PAUSBK_Dx

source_name: pediatric AML sample 50


title: gDNA from diagnosic pediatric AML 57

description:
pediatric AML
PAUTIK_Dx

source_name: pediatric AML sample 57


title: WT_0_R2


title: 101_Muscle


title: gDNA from diagnosic pediatric AML 53

description:
pediatric AML
PAUSKR_Dx

source_name: pediatric AML sample 53


title: 96_Muscle


title: gDNA from diagnosic pediatric AML 52

description:
pediatric AML
PAUSCS_Dx

source_name: pediatric AML sample 52


title: 97_Muscle


title: gDNA from diagnosic pediatric AML 49

description:
pediatric AML
PAUSBA_Dx

source_name: pediatric AML sample 49


title: 98_Muscle


title: gDNA from diagnosic pediatric AML 62

description:
pediatric AML
PAUUHV_Dx

source_name: pediatric AML sample 62


title: gDNA from diagnosic pediatric AML 55

description:
pediatric AML
PAUSXS_Dx

source_name: pediatric AML sample 55


title: gDNA from diagnosic pediatric AML 51

description:
pediatric AML
PAUSFM_Dx

source_name: pediatric AML sample 51


title: gDNA from diagnosic pediatric AML 48

description:
pediatric AML
PAURWH_Dx

source_name: pediatric AML sample 48


title: gDNA from diagnosic pediatric AML 46

description:
pediatric AML
PAURUT_Dx

source_name: pediatric AML sample 46


title: gDNA from diagnosic pediatric AML 47

description:
pediatric AML
PAURVI_Dx

source_name: pediatric AML sample 47


title: gDNA from diagnosic pediatric AML 41

description:
pediatric AML
PAURDN_Dx

source_name: pediatric AML sample 41


title: gDNA from diagnosic pediatric AML 38

description:
pediatric AML
PAUPXH_Dx

source_name: pediatric AML sample 38


title: gDNA from diagnosic pediatric AML 40

description:
pediatric AML
PAUPYX_Dx

source_name: pediatric AML sample 40


title: gDNA from diagnosic pediatric AML 42

description:
pediatric AML
PAURII_Dx

source_name: pediatric AML sample 42


title: gDNA from diagnosic pediatric AML 37

description:
pediatric AML
PAUPSX_Dx

source_name: pediatric AML sample 37


title: gDNA from diagnosic pediatric AML 44

description:
pediatric AML
PAURJZ_Dx

source_name: pediatric AML sample 44


title: gDNA from diagnosic pediatric AML 43

description:
pediatric AML
PAURJK_Dx

source_name: pediatric AML sample 43


title: gDNA from diagnosic pediatric AML 36

description:
pediatric AML
PAULTY_Dx

source_name: pediatric AML sample 36


title: 91_Muscle

source_name: Muscle HIAC

value: High Inherent Aerobic Capacity (HIAC)


title: 94_Muscle


title: gDNA from diagnosic pediatric AML 45

description:
pediatric AML
PAURLB_Dx

source_name: pediatric AML sample 45


title: 95_Muscle

source_name: Muscle LIAC


title: gDNA from diagnosic pediatric AML 39

description:
pediatric AML
PAURAS_Dx

source_name: pediatric AML sample 39


title: 92_Muscle


title: 93_Muscle


title: gDNA from diagnosic pediatric AML 35

description:
pediatric AML
PAUPNN_Dx

source_name: pediatric AML sample 35


title: 90_Muscle


title: gDNA from diagnosic pediatric AML 33

description:
pediatric AML
PAUPNA_Dx

source_name: pediatric AML sample 33


title: gDNA from diagnosic pediatric AML 34

description:
pediatric AML
PAUPPD_Dx

source_name: pediatric AML sample 34


title: 89_Muscle


title: gDNA from diagnosic pediatric AML 31

description:
pediatric AML
PAUPDK_Dx

source_name: pediatric AML sample 31


title: gDNA from diagnosic pediatric AML 32

description:
pediatric AML
PAUPIY_Dx

source_name: pediatric AML sample 32


title: 87_Muscle


title: gDNA from diagnosic pediatric AML 29

description:
pediatric AML
PAUNVK_Dx

source_name: pediatric AML sample 29


title: gDNA from diagnosic pediatric AML 30

description:
pediatric AML
PAUPDB_Dx

source_name: pediatric AML sample 30


title: gDNA from diagnosic pediatric AML 28

description:
pediatric AML
PAUNYL_Dx

source_name: pediatric AML sample 28


title: 86_Muscle


title: 85_Muscle


title: 43_MG

source_name: Mammary gland LIAC

value: mammary gland


title: gDNA from diagnosic pediatric AML 21

description:
pediatric AML
PAUMUZ_Dx

source_name: pediatric AML sample 21


title: gDNA from diagnosic pediatric AML 27

description:
pediatric AML
PAUNTD_Dx

source_name: pediatric AML sample 27


title: gDNA from diagnosic pediatric AML 26

description:
pediatric AML
PAUNSV_Dx

source_name: pediatric AML sample 26


title: gDNA from diagnosic pediatric AML 20

description:
pediatric AML
PAUMTZ_Dx

source_name: pediatric AML sample 20


title: gDNA from diagnosic pediatric AML 19

description:
pediatric AML
PAUMMR_Dx

source_name: pediatric AML sample 19


title: gDNA from diagnosic pediatric AML 23

description:
pediatric AML
PAUNBY_Dx

source_name: pediatric AML sample 23


title: gDNA from diagnosic pediatric AML 24

description:
pediatric AML
PAUNDC_Dx

source_name: pediatric AML sample 24


title: gDNA from diagnosic pediatric AML 17

description:
pediatric AML
PAUMGZ_Dx

source_name: pediatric AML sample 17


title: gDNA from diagnosic pediatric AML 16

description:
pediatric AML
PAUMIH_Dx

source_name: pediatric AML sample 16


title: 88_Muscle

source_name: Muscle HIAC


title: gDNA from diagnosic pediatric AML 18

description:
pediatric AML
PAUMJB_Dx

source_name: pediatric AML sample 18


title: gDNA from diagnosic pediatric AML 22

description:
pediatric AML
PAUNBR_Dx

source_name: pediatric AML sample 22


title: 40_MG


title: 39_MG


title: 41_MG


title: gDNA from diagnosic pediatric AML 13

description:
pediatric AML
PAULRS_Dx

source_name: pediatric AML sample 13


title: gDNA from diagnosic pediatric AML 14

description:
pediatric AML
PAUMAD_Dx

source_name: pediatric AML sample 14

value: FUS-ERG


title: gDNA from diagnosic pediatric AML 15

description:
pediatric AML
PAUMCV_Dx

source_name: pediatric AML sample 15


title: 38_MG


title: gDNA from diagnosic pediatric AML 12

description:
pediatric AML
PAULSL_Dx

source_name: pediatric AML sample 12


title: gDNA from diagnosic pediatric AML 25

description:
pediatric AML
PAUNHG_Dx

source_name: pediatric AML sample 25

value: Male


title: gDNA from diagnosic pediatric AML 10

description:
pediatric AML
PAULDS_Dx

source_name: pediatric AML sample 10

value: Diagnosis


title: gDNA from diagnosic pediatric AML 11

description:
pediatric AML
PAULNJ_Dx

source_name: pediatric AML sample 11


title: 37_MG

source_name: Mammary gland LIAC


title: 42_MG


title: 36_MG


title: gDNA from diagnosic pediatric AML 9

description:
pediatric AML
PAULCA_Dx

source_name: pediatric AML sample 9

value: Female


title: gDNA from diagnosic pediatric AML 8

description:
pediatric AML
PAUKTH_Dx

source_name: pediatric AML sample 8


title: gDNA from diagnosic pediatric AML 4

description:
pediatric AML
PAUJMC_Dx

source_name: pediatric AML sample 4


title: gDNA from diagnosic pediatric AML 3

description:
pediatric AML
PAUJCF_Dx

source_name: pediatric AML sample 3


title: gDNA from diagnosic pediatric AML 6

description:
pediatric AML
PAUKDH_Dx

source_name: pediatric AML sample 6


title: 33_MG

source_name: Mammary gland HIAC


title: 34_MG


title: gDNA from diagnosic pediatric AML 5

description:
pediatric AML
PAUJNJ_Dx

source_name: pediatric AML sample 5


title: 32_MG


title: 31_MG


title: gDNA from diagnosic pediatric AML 2

description:
pediatric AML
PAUHXN_Dx

source_name: pediatric AML sample 2


title: gDNA from diagnosic pediatric AML 1

description:
pediatric AML
PAUHFI_Dx

source_name: pediatric AML sample 1


title: 29_MG


title: 28_MG


title: 27_MG


title: 35_MG


title: 26_MG


title: gDNA from diagnosic pediatric AML 7

description:
pediatric AML
PAUKEZ_Dx

source_name: pediatric AML sample 7


title: 25_MG


title: 24_MG


title: 23_MG


title: 22_MG


title: 30_MG


title: 20_Tumor

source_name: Mammary tumor LIAC

value: mammary tumor


title: 19_Tumor


title: gDNA from diagnosic pediatric AML 54

description:
pediatric AML
PAUSTM_Dx

source_name: pediatric AML sample 54


title: 18_Tumor


title: 17_Tumor


title: [EPIC] genomic DNA from muscle sample 77

city: Oxford

first: Elie

last: Antoun

state: United Kingdom

address: Nuffield Department of Medicine

department: CAMS China Oxford Institute (CAMS-COI

country: United Kingdom

institute: University of Oxford

description: muscle sample

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

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

source_name: muscle sample 77

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from the HSS muscle tissue using QIAamp DNA mini kit (Qiagen) and from the HSSe muscle tissue using the high salt method.

tag: cohort

value: HSSe

tag: sample type

value: Muscle tissue

tag: age (yr)

tag: dna extraction method

value: High salt


title: [EPIC] genomic DNA from muscle sample 69

description: muscle sample

source_name: muscle sample 69

value: HSS

value: QIAamp


title: [EPIC] genomic DNA from muscle sample 76

description: muscle sample

source_name: muscle sample 76


title: [EPIC] genomic DNA from muscle sample 59

description: muscle sample

source_name: muscle sample 59


title: [EPIC] genomic DNA from muscle sample 65

description: muscle sample

source_name: muscle sample 65


title: [EPIC] genomic DNA from muscle sample 58

description: muscle sample

source_name: muscle sample 58


title: [EPIC] genomic DNA from muscle sample 66

description: muscle sample

source_name: muscle sample 66


title: [EPIC] genomic DNA from muscle sample 74

description: muscle sample

source_name: muscle sample 74


title: [EPIC] genomic DNA from muscle sample 72

description: muscle sample

source_name: muscle sample 72


title: [EPIC] genomic DNA from muscle sample 68

description: muscle sample

source_name: muscle sample 68


title: [EPIC] genomic DNA from muscle sample 67

description: muscle sample

source_name: muscle sample 67


title: [EPIC] genomic DNA from muscle sample 55

description: muscle sample

source_name: muscle sample 55


title: 15_Tumor

source_name: Mammary tumor HIAC


title: [EPIC] genomic DNA from muscle sample 61

description: muscle sample

source_name: muscle sample 61


title: [EPIC] genomic DNA from muscle sample 71

description: muscle sample

source_name: muscle sample 71


title: 14_Tumor


title: [EPIC] genomic DNA from muscle sample 56

description: muscle sample

source_name: muscle sample 56


title: [EPIC] genomic DNA from muscle sample 73

description: muscle sample

source_name: muscle sample 73


title: [EPIC] genomic DNA from muscle sample 78

description: muscle sample

source_name: muscle sample 78


title: 8_Tumor

source_name: Mammary tumor LIAC


title: [EPIC] genomic DNA from muscle sample 75

description: muscle sample

source_name: muscle sample 75


title: [EPIC] genomic DNA from muscle sample 60

description: muscle sample

source_name: muscle sample 60


title: 7_Tumor


title: [EPIC] genomic DNA from muscle sample 62

description: muscle sample

source_name: muscle sample 62


title: [EPIC] genomic DNA from muscle sample 52

description: muscle sample

source_name: muscle sample 52


title: 16_Tumor


title: [EPIC] genomic DNA from muscle sample 64

description: muscle sample

source_name: muscle sample 64


title: 13_Tumor


title: 4_Tumor


title: 6_Tumor


title: 5_Tumor


title: [EPIC] genomic DNA from muscle sample 57

description: muscle sample

source_name: muscle sample 57


title: [EPIC] genomic DNA from muscle sample 53

description: muscle sample

source_name: muscle sample 53


title: [EPIC] genomic DNA from muscle sample 51

description: muscle sample

source_name: muscle sample 51


title: [EPIC] genomic DNA from muscle sample 63

description: muscle sample

source_name: muscle sample 63


title: 3_Tumor


title: 2_Tumor


title: [EPIC] genomic DNA from muscle sample 50

description: muscle sample

source_name: muscle sample 50


title: [EPIC] genomic DNA from muscle sample 70

description: muscle sample

source_name: muscle sample 70


title: PB-Diff

city: Tianjin

first: Ling

last: Shuai

address: 38 Tong Yan Road, Jinnan district

department: State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy

country: China

institute: Nankai University

description: PCR production

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: Rattus_norvegicus_Ensemble_103
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: embryonic stem cells

extract_protocol:
Cell samples were collected and RNA was harvested using Trizol reagent. NEB Next® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5 min at 95 °Cbefore PCR. Then PCR was performed with Phusion High -Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
PCR-free library

tag: cell type

value: embryonic stem cells

value: after screening


title: [EPIC] genomic DNA from muscle sample 54

description: muscle sample

source_name: muscle sample 54


title: 1_Tumor

source_name: Mammary tumor HIAC


title: Chow5

city: Winston-Salem

first: Jeannie

last: Chan

state: NC

address: Medical Center Boulevard

department: Internal Medicine

institute: Wake Forest School of Medicine

data_processing:
Raw sequences were de-multiplexed using the Illumina Casava v1.8 software.
FastQC and FASTX-toolkit were used for QC. Sequence reads with Phred scores ≥ Q30 were retained.
Sequence reads were aligned against the vervet reference genome (ChlSab1.1) using STAR 2.5.3a.
Aligned reads were quantified using an expectation-maximization algorithm in Partek Flow and annotated using the Ensembl release 93 gene model.
Transcript abundances were normalized by the Trimmed mean of M-values method.
Genome_build: ChlSab1.1
Supplementary_files_format_and_content: Matrix table of transcript counts before normalization for all genes in 10 samples.
Supplementary_files_format_and_content: Matrix table of transcript counts after normalization for all genes in 10 samples.

organism: Chlorocebus sabaeus

source_name: Liver

extract_protocol:
Liver tissue was flash frozen in liquid nitrogen immediately after collection and stored at -80oC. Total RNA was extracted from vervet monkey livers using the Zymo Direct-zol RNA MiniPrep kit.
RNA-Seq libraries were prepared from 500 ng of total RNA according to the Illumina TruSeq stranded mRNA protocol.

treatment_protocol: Prior to the study, all animals were maintained on a chow diet. In the study, 5 animals were fed a high fructose diet and 5 were fed a chow diet.

tag: diet

value: Chow


title: PB-Ctrl

description: PCR production

value: before screening


title: [EPIC] genomic DNA from muscle sample 47

description: muscle sample

source_name: muscle sample 47


title: [EPIC] genomic DNA from muscle sample 44

description: muscle sample

source_name: muscle sample 44


title: Chow4

value: female


title: [EPIC] genomic DNA from muscle sample 46

description: muscle sample

source_name: muscle sample 46


title: [EPIC] genomic DNA from muscle sample 48

description: muscle sample

source_name: muscle sample 48


title: [EPIC] genomic DNA from muscle sample 49

description: muscle sample

source_name: muscle sample 49


title: [EPIC] genomic DNA from muscle sample 42

description: muscle sample

source_name: muscle sample 42


title: [EPIC] genomic DNA from muscle sample 38

description: muscle sample

source_name: muscle sample 38


title: [EPIC] genomic DNA from muscle sample 41

description: muscle sample

source_name: muscle sample 41


title: HFr5

value: High fructose


title: [EPIC] genomic DNA from muscle sample 43

description: muscle sample

source_name: muscle sample 43


title: [EPIC] genomic DNA from muscle sample 32

description: muscle sample

source_name: muscle sample 32


title: [EPIC] genomic DNA from muscle sample 39

description: muscle sample

source_name: muscle sample 39


title: [EPIC] genomic DNA from muscle sample 35

description: muscle sample

source_name: muscle sample 35


title: [EPIC] genomic DNA from muscle sample 45

description: muscle sample

source_name: muscle sample 45


title: [EPIC] genomic DNA from muscle sample 33

description: muscle sample

source_name: muscle sample 33


title: Chow3


title: [EPIC] genomic DNA from muscle sample 34

description: muscle sample

source_name: muscle sample 34


title: Chow2


title: [EPIC] genomic DNA from muscle sample 30

description: muscle sample

source_name: muscle sample 30


title: Chow1

source_name: Liver


title: [EPIC] genomic DNA from muscle sample 29

description: muscle sample

source_name: muscle sample 29


title: [EPIC] genomic DNA from muscle sample 28

description: muscle sample

source_name: muscle sample 28


title: HFr4


title: HFr3


title: [EPIC] genomic DNA from muscle sample 31

description: muscle sample

source_name: muscle sample 31


title: HFr2


title: [EPIC] genomic DNA from muscle sample 26

description: muscle sample

source_name: muscle sample 26


title: HFr1


title: [EPIC] genomic DNA from muscle sample 40

description: muscle sample

source_name: muscle sample 40


title: [EPIC] genomic DNA from muscle sample 37

description: muscle sample

source_name: muscle sample 37


title: Truncated ZFP3_F1-F10 construct replicate 2

city: Palo Alto

first: Zheng

last: Zuo

state: CA

address: Stanford

department: Genetics

institute: Stanford university

library_source: genomic

data_processing:
Library strategy: Spec-seq
[Preliminary processing for each sample]  Counting the number of Bound and Unbound reads for each sample. The negative logarithmic ratio of Bound and Unbound reads can be calculated as the relative binding energy for each binding sites.
[Data quality check between replicates]  Cross comparison between replicate samples reveals the resolution of each sample, usually around 0.2kT for individual site.
[Specificity and methylation sensitivity analysis]  The motif or specificity profile can be constructed by regression of binding energy values of select sequences, e.g., some reference site and all of its single/double variants. TFCookbook package, which contains all necessary codes to analyze the TF-DNA motif profile, can be accessed through https://github.com/zeropin/zeropin/TFCookbook.
Supplementary_files_format_and_content: Processed data files for each ZFP and analysis workflow for ZNF140
Supplementary_files_format_and_content: For each sample, the associated csv file contains the bound and unbound reads, calculated relative binding energy, library type, and the number of mismatches to some reference site for individual binding site. The data analysis protocol for each ZFP can be accessed through Github https://github.com/zeropin/ZFPCookbook

molecule: other

organism: synthetic construct

source_name: Spec-seq sample to synthetic DNA library

extract_protocol:
[Recombinant protein expression protocol] We used the NEB PURExpress or E. coli_BL21 system to produce N-terminal HALO tagged ZFP constructs and noticed better success rates than previously used SUMO-tagged constructs.
[EMSA protocol] 20uL binding reactions were loaded onto 10% Tris-glycine gel in cold room and run for 50mins at 200V.
[Sequencing sample prep protocol] The bound and unbound fractions of each sample were cut separately as thin gel slice, extracted by acrylamide gel extraction buffer _soaking a 55C for more than 30mins. Each fraction of DNA pool was purified and further amplified by uniquely indexed Illumina primers set for at least 12 cycles _annealing temperature 52C, extension time 30s. All samples were pooled together for Illumina Nextseq _1X 75bp single end run.

tag: recombinant protein

value: Truncated ZFP3_F1-F10 construct


title: Paenibacillus_Gnotobiotic adults rep3 [pa.ad9]

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11.Only sequences ≥25 nucleotides (nt) in length were considered for further analysis.
STAR version 2.5.0a, with default parameters, was used for alignment on the Ae. aegypti genome
Genes were counted using featureCounts version 1.4.6-p35from Subreads package (parameters:  -t exon, -g gene_id and -s 1)
Count data were analyzed using R version 3.6.1 and the Bioconductor package DESeq2 version 1.24.0. The normalization and dispersion estimation were performed with DESeq2 using the default parameter and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between gnotobiotic and non-axenic for larval, pupal and adult stages. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with both an absolute log2FC > 1 and an adjusted p-value lower than 0.05 were considered differentially expressed.
Genome_build: AaegL5.3, http://vectorbase.org
Supplementary_files_format_and_content: Count matrix from DESeq2

organism: Aedes aegypti

growth_protocol: Aedes aegypti eggs were surface sterilized and were allowed to hatch in sterile water in a vacuum chamber, then were transferred to sterile 25-ml tissue-culture flasks with filter-top lids and maintained in 15 ml of sterile water. Larvae were maintained on 60 μl of sterile fish food (autoclaved food for 20 min) every other day.

extract_protocol:
Pool of 12 axenic larvae, L4 larvae, pupae and adult mosquitoes were surface sterilized and total RNA was extracted using Trizol.
Axenic larva, L4 larva, pupa and adult mosquito libraries for controls (non-axenics) and for gnotobiotics (Flavobacterium, Enterobacteriaceae, Lysobacter and Paenibacillus treatments) were prepared from total RNA of pool of 12 individuals. Removal of ribosomal RNA, fragmentation and library preparation were performed by using the TruSeq Stranded mRNA library preparation kit (Illumina) following manufacturer’s instructions. Libraries quality was checked on a DNA1000 Bioanalyzer chip (Agilent) and quantification made by QuBit DNA HS kit (ThermoFisher). single reads of 65 nucleotides in length (à verifier) were generated on a HiSeq2500 sequencing platform (Illumina).

treatment_protocol: Axenic larvae were made gnotobiotic larvae by adding to the flask 5.10E5 CFU/ml of selected bacterial isolates.

tag: treatment

value: Paenibacillus

tag: Stage

value: Adults


title: [EPIC] genomic DNA from muscle sample 22

description: muscle sample

source_name: muscle sample 22

value: Male


title: Truncated ZFP3_F1-F10 construct replicate 1


title: Paenibacillus_Gnotobiotic adults rep2 [pa.ad8]


title: Paenibacillus_Gnotobiotic adults rep1 [pa.ad7]


title: Truncated ZNF140_F1-F6 construct replicate 2

value: Truncated ZNF140_F1-F6 construct


title: [EPIC] genomic DNA from muscle sample 21

description: muscle sample

source_name: muscle sample 21


title: [EPIC] genomic DNA from muscle sample 25

description: muscle sample

source_name: muscle sample 25


title: [EPIC] genomic DNA from muscle sample 20

description: muscle sample

source_name: muscle sample 20


title: [EPIC] genomic DNA from muscle sample 36

description: muscle sample

source_name: muscle sample 36


title: [EPIC] genomic DNA from muscle sample 24

description: muscle sample

source_name: muscle sample 24


title: Paenibacillus_Gnotobiotic pupae rep2 [pa.pup5]

value: Pupae


title: [EPIC] genomic DNA from muscle sample 23

description: muscle sample

source_name: muscle sample 23


title: [EPIC] genomic DNA from muscle sample 10

description: muscle sample

source_name: muscle sample 10

value: HSSe


title: [EPIC] genomic DNA from muscle sample 18

description: muscle sample

source_name: muscle sample 18

value: Muscle tissue


title: [EPIC] genomic DNA from muscle sample 16

description: muscle sample

source_name: muscle sample 16


title: [EPIC] genomic DNA from muscle sample 14

description: muscle sample

source_name: muscle sample 14

value: High salt


title: Paenibacillus_Gnotobiotic larvae rep3 [pa.lar3]

value: L4 Larvae


title: Truncated ZNF140_F1-F6 construct replicate 1


title: [EPIC] genomic DNA from muscle sample 5

description: muscle sample

source_name: muscle sample 5

value: HSS

value: QIAamp


title: Paenibacillus_Gnotobiotic pupae rep1 [pa.pup4]


title: [EPIC] genomic DNA from muscle sample 13

description: muscle sample

source_name: muscle sample 13


title: Paenibacillus_Gnotobiotic larvae rep2 [pa.lar2]


title: [EPIC] genomic DNA from muscle sample 12

description: muscle sample

source_name: muscle sample 12


title: 59A_Malignant melanoma of the skin

city: Budapest

first: Laura

last: Vizkeleti

address: Üllői str. 93.

department: 2nd Deptartment of Pathology

country: Hungary

institute: Semmelweis University

description: Hybridized to OncoScan

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the recent laboratory protocol of UD GenoMed Medical Genomic Technologies Ltd. (Clinical Genomic Center, University of Debrecen, Debrecen, Hungary).

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations FS450, and scanned using the Gene Chip Scanner 3000.

data_processing: Raw data passed quality control were further analyzed by Affymetrix® Chromosome Analysis Suite (Affymetrix, Santa Clara, CA, US). CEL files were generated from the scanned array image files by the Affymetrix GeneChip Command Console Software and were imported into the Affymetrix Chromosome Analysis Suite v4.2.0.80 Software. CNV data were analyzed with the Nexus Copy Number software (BioDiscovery, CA, ver. 8).

label: Biotin

source_name: Malignant melanoma tissue, FFPE archived, diagnostic

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from frozen autopsy or FFPE archived diagnostic melanoma tissue samples using the QIAamp DNA Mini and QIAamp DNA FFPE Tissue Kits, respectively. DNA quality and quantity was assessed using a NanoDrop ND-1000 UV–visible spectrophotometer and Qubit dsDNA HS Assay on a Qubit 1.0 fluorometer. Fragment analysis of DNA was carried out applying 1% agarose gel electrophoresis as well as BioAnalyzer 2100 using High Sensitivity DNA Kit.

value: malignant melanoma


title: Non-axenic adults rep2 [na.ad8]

value: Non-axenic/control


title: [EPIC] genomic DNA from muscle sample 6

description: muscle sample

source_name: muscle sample 6


title: 57A_Malignant melanoma of the skin

description: Hybridized to OncoScan


title: Non-axenic adults rep1 [na.ad7]


title: Non-axenic pupae rep2 [na.pup5]


title: Non-axenic pupae rep1 [na.pup4]


title: [EPIC] genomic DNA from muscle sample 4

description: muscle sample

source_name: muscle sample 4


title: Paenibacillus_Gnotobiotic larvae rep1 [pa.lar1]


title: [EPIC] genomic DNA from muscle sample 7

description: muscle sample

source_name: muscle sample 7


title: Non-axenic adults rep3 [na.ad9]


title: Non-axenic pupae rep3 [na.pup6]


title: [EPIC] genomic DNA from muscle sample 8

description: muscle sample

source_name: muscle sample 8


title: 56A_Malignant melanoma of the skin

description: Hybridized to OncoScan


title: [EPIC] genomic DNA from muscle sample 27

description: muscle sample

source_name: muscle sample 27


title: Non-axenic larvae rep2 [na.lar2]


title: 55A_Malignant melanoma of the skin

description: Hybridized to OncoScan


title: Lysobacter_Gnotobiotic adults rep3 [lys.ad9]

value: Lysobacter


title: 53A_Malignant melanoma of the skin

description: Hybridized to OncoScan


title: 53B_Malignant melanoma of the skin

description: Hybridized to OncoScan


title: Lysobacter_Gnotobiotic adults rep1 [lys.ad7]


title: 59B_Malignant melanoma of the skin

description: Hybridized to OncoScan

source_name: Malignant melanoma tissue, cryopreserved, autopsy


title: [EPIC] genomic DNA from muscle sample 2

description: muscle sample

source_name: muscle sample 2


title: Non-axenic larvae rep3 [na.lar3]


title: Lysobacter_Gnotobiotic adults rep2 [lys.ad8]


title: 48B_Malignant melanoma of the skin

description: Hybridized to OncoScan


title: Lysobacter_Gnotobiotic pupae rep3 [lys.pup6]


title: Paenibacillus_Gnotobiotic pupae rep3 [pa.pup6]


title: [EPIC] genomic DNA from muscle sample 11

description: muscle sample

source_name: muscle sample 11


title: [EPIC] genomic DNA from muscle sample 1

description: muscle sample

source_name: muscle sample 1


title: Lysobacter_Gnotobiotic pupae rep2 [lys.pup5]


title: 48A_Malignant melanoma of the skin

description: Hybridized to OncoScan


title: 33D_Malignant melanoma of the skin

description: Hybridized to OncoScan


title: Lysobacter_Gnotobiotic pupae rep1 [lys.pup4]


title: Lysobacter_Gnotobiotic larvae rep3 [lys.lar3]


title: Lysobacter_Gnotobiotic larvae rep2 [lys.lar2]


title: Flavobacterium_Gnotobiotic adults rep3 [fla.ad9]

value: Flavobacterium


title: Flavobacterium_Gnotobiotic adults rep2 [fla.ad8]


title: 33B_Malignant melanoma of the skin

description: Hybridized to OncoScan


title: Flavobacterium_Gnotobiotic adults rep1 [fla.ad7]


title: [EPIC] genomic DNA from muscle sample 17

description: muscle sample

source_name: muscle sample 17


title: [EPIC] genomic DNA from muscle sample 15

description: muscle sample

source_name: muscle sample 15


title: Lysobacter_Gnotobiotic larvae rep1 [lys.lar1]


title: [EPIC] genomic DNA from muscle sample 9

description: muscle sample

source_name: muscle sample 9


title: 32A_Malignant melanoma of the skin

description: Hybridized to OncoScan


title: 32E_Malignant melanoma of the skin

description: Hybridized to OncoScan


title: 32B_Malignant melanoma of the skin

description: Hybridized to OncoScan


title: Flavobacterium_Gnotobiotic pupae rep2 [fla.pup5]


title: Flavobacterium_Gnotobiotic larvae rep2 [fla.lar2]


title: Flavobacterium_Gnotobiotic larvae rep3 [fla.lar3]


title: Flavobacterium_Gnotobiotic larvae rep1 [fla.lar1]


title: Flavobacterium_Gnotobiotic pupae rep1 [fla.pup4]


title: Flavobacterium_Gnotobiotic pupae rep3 [fla.pup6]


title: Enterobacteriaceae_Gnotobiotic adults rep3 [ent.ad9]

value: Enterobacteriaceae


title: Enterobacteriaceae_Gnotobiotic adults rep2 [ent.ad8]


title: 28B_Malignant melanoma of the skin

description: Hybridized to OncoScan


title: [EPIC] genomic DNA from muscle sample 19

description: muscle sample

source_name: muscle sample 19


title: Enterobacteriaceae_Gnotobiotic adults rep1 [ent.ad7]


title: Enterobacteriaceae_Gnotobiotic pupae rep3 [ent.pup6]


title: 28C_Malignant melanoma of the skin

description: Hybridized to OncoScan


title: 24C_Malignant melanoma of the skin

description: Hybridized to OncoScan


title: [EPIC] genomic DNA from muscle sample 3

description: muscle sample

source_name: muscle sample 3


title: Enterobacteriaceae_Gnotobiotic larvae rep3 [ent.lar3]


title: Enterobacteriaceae_Gnotobiotic larvae rep2 [ent.lar2]


title: 24B_Malignant melanoma of the skin

description: Hybridized to OncoScan


title: Enterobacteriaceae_Gnotobiotic pupae rep1 [ent.pup4]


title: Enterobacteriaceae_Gnotobiotic larvae rep1 [ent.lar1]


title: 24A_Malignant melanoma of the skin

description: Hybridized to OncoScan


title: Axenic larvae rep2 [ax.lar2]

source_name: Axenic larvae

value: axenic

value: L1 Larvae


title: Axenic larvae rep3 [ax.lar3]


title: 19A_Malignant melanoma of the skin

description: Hybridized to OncoScan


title: 5 mM 3-MA + 150 mM NaCl treated wheat leaves rep2

first: Jieyu

last: Yue

state: Tianjin

address: Road Binshuixidao NO.393

institute: Tianjin Normal University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions.
The Triticum aestivum L. reference genome and gene model annotation files were downloaded from ftp://ftp.ensemblgenomes.org/pub/release-45/plants/fasta/triticum_aestivum/dna/Triticum_aestivum.IWGSC.dna.toplevel.fa.gz. The paired-end clean RNA-seq reads were aligned to the reference genome using Hisat2 (version 2.0.5,) was used to count the number of reads mapped to each gene.
Genome_build: ftp://ftp.ensemblgenomes.org/pub/release-45/plants/fasta/triticum_aestivum/dna/Triticum_aestivum.IWGSC.dna.toplevel.fa.gz
Supplementary_files_format_and_content: ExpressionProfile.txt: Matrix table with raw gene counts and FPKM values for every gene and every sample.

organism: Triticum aestivum

source_name: Triticum aestivum L.

growth_protocol: The test species were NaCl-tolerant Jimai 22 wheat varieties. Jimai 22 is a medium gluten wheat variety with super high yield, multi resistance and high quality. The Jimai 22 seeds were first washed with tap water and then rinsed with distilled water thrice before being soaked in distilled water for 12 h. The seeds were then germinated on moist gauze. A small amount of distilled water was sprayed onto the seeds for culture at ambient temperature. The distilled water was changed every 24 h until the seedlings grew to the one-leaf-and-one-bud stage. The uniform seedlings were transplanted into plastic pots containing 1/4 Hoagland solution for further culture. The nutrient solution was changed every 2 d until the seedlings grew to the two-leaf-and-one-bud stage.

extract_protocol:
The roots and leaves samples were flash frozen on dry ice respectively, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The seedlings selected for uniform growth were separately transplanted into plastic pots (50 cm in diameter and 40 cm in height; 10 plants per pot) containing the 1/4 Hoagland nutrient solution (pH 5.2) with 0 μM NaCl to form the control group and various types of stress (150 mM NaCl, 5 mM 3-MA, or 5 mM 3-MA+ 150 mM NaCl) to form the NaCl treatment groups. 3-MA (Sigma Aldrich, Saint Louis, MO, USA) was added to the medium 5 h prior to NaCl treatment. The nutrient solution was changed every 2 d. For each treatment, seedlings from three pots were separately sampled or measured as replicates. Four days after NaCl and 3-MA treatment, the roots and the third leaves were collected respectively with every 10 of them being mixed as one biological replicate for each treatment. Every treatment had four biological replicates. Each sample was ground respectively into powder in a mortar using liquid nitrogen. Total RNA was extracted from samples using a Trizol reagent (Invitrogen). There were six sample groups, including CG: the control wheat roots, TG: 150 mM NaCl treated wheat roots, TMG: 5 mM 3-MA + 150 mM NaCl treated wheat roots, CY: the control wheat leaves, TY: 150 mM NaCl treated wheat leaves, and TMY: 5 mM 3-MA + 150 mM NaCl treated wheat leaves.

tag: variety

value: Jimai 22

value: leaf

value: 5 mM 3-MA + 150 mM NaCl

tag: time point

value: four days after treatment


title: 5 mM 3-MA + 150 mM NaCl treated wheat leaves rep3

tag: tissue


title: 63129: D. melanogaster macrophages_CG9005 mutant_Rep3

city: Klosterneuburg

first: Daria

last: Siekhaus

address: Am Campus 1

department: Bertalanffy Building

country: Austria

institute: IST Austria

description: FACS-sorted labled macrophages

data_processing:
Aligning the transcriptome sequence reads to the D. melanogaster reference genome (Ensembl BDGP6) with STAR version 2.5.1b using 2-pass alignment mode.
Counting the number of reads; the quality of the RNA-seq library was assessed by calculating the percentage of reads that are mapped  to exonic and intronic regions of the genome, while using polyA selection for library preparation.
the reads were associated with known genes and the number of reads aligned within each gene was counted using HTSeq tool version 0.5.4p3.
the counts were normalised using the TMM normalisation method of the edgeR R/Bioconductor package ( (R version 3.4.4, Bioconductor version 3.6)
The data were  log transformed using the voom approach in the limma package. For the visualizations and result files the TMM normalised counts are represented as TPM (Transcripts Per Kilobase Million) values.
Genome_build: the Drosophila melanogaster reference genome (Ensembl BDGP6)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for both wildtype and the mutant  samples

organism: Drosophila melanogaster

source_name: Embryonic macrophages

growth_protocol: Fly embryos of both genotypes were collected for stage 11 at 29°C.

extract_protocol:
Total RNA was isolated from FACS-sorted mCherry-positive macrophages using Rneasy Plus Micro Kit (QIAGEN) and stored at -80C for quality control and RNA sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina’s HiSeq2500, 50bp read length)

treatment_protocol: Dechorionated embryos were dissociated and Cherry-positive macrophages were sorted by FACS using the protocol from Attila Gyoergy et al., G3, 2018.

tag: developmental stage

value: Embryonic macrophages from stage 17

value: Embryonic macrophages (hemocytes)

tag: genotype

value: 3xMcherry-tagged macrophages


title: 63130: D. melanogaster macrophages_CG9005 mutant_Rep4

description: FACS-sorted labled macrophages

value: Embryonic macrophages from stage 18


title: 63128: D. melanogaster macrophages_CG9005 mutant_Rep2

description: FACS-sorted labled macrophages

value: Embryonic macrophages from stage 16


title: 5 mM 3-MA + 150 mM NaCl treated wheat roots rep3

value: root


title: 5 mM 3-MA + 150 mM NaCl treated wheat roots rep2


title: Enterobacteriaceae_Gnotobiotic pupae rep2 [ent.pup5]

value: Pupae


title: 63125: D. melanogaster macrophages_WT_Rep3

description: FACS-sorted labled macrophages

value: Embryonic macrophages from stage 13


title: 63127: D. melanogaster macrophages_CG9005 mutant_Rep1

description: FACS-sorted labled macrophages

value: Embryonic macrophages from stage 15


title: 63126: D. melanogaster macrophages_WT_Rep4

description: FACS-sorted labled macrophages

value: Embryonic macrophages from stage 14


title: 33A_Malignant melanoma of the skin

description: Hybridized to OncoScan

source_name: Malignant melanoma tissue, FFPE archived, diagnostic

value: malignant melanoma


title: 150 mM NaCl treated wheat leaves rep3

value: 150 mM NaCl


title: 150 mM NaCl treated wheat leaves rep1


title: control wheat leaves rep2

value: Control


title: control wheat roots rep3

value: Jimai 22


title: control wheat roots rep2


title: 63124: D. melanogaster macrophages_WT_Rep2

description: FACS-sorted labled macrophages

value: Embryonic macrophages from stage 12


title: 63123: D. melanogaster macrophages_WT_Rep1

description: FACS-sorted labled macrophages

value: Embryonic macrophages from stage 11


title: control wheat leaves rep1

value: leaf

value: four days after treatment


title: 5 mM 3-MA + 150 mM NaCl treated wheat roots rep1

value: 5 mM 3-MA + 150 mM NaCl


title: 150 mM NaCl treated wheat leaves rep2


title: 150 mM NaCl treated wheat roots rep1


title: 150 mM NaCl treated wheat roots rep3


title: control wheat leaves rep3


title: Truncated ZNF10_F1-F8 construct replicate 2

source_name: Spec-seq sample to synthetic DNA library

value: Truncated ZNF10_F1-F8 construct


title: Axenic larvae rep1 [ax.lar1]

value: axenic

value: L1 Larvae


title: 5 mM 3-MA + 150 mM NaCl treated wheat leaves rep1


title: Truncated ZNF10_F1-F8 construct replicate 1


title: control wheat roots rep1

value: root


title: AH_33

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: aa.buccal.results.csv.gz, comb.buccal.results.csv.gz

data_processing:
Basic read quality was verified using summaries produced by FastQC. Trimmomatic was used to remove low quality reads and bases
The reads for each sample were mapped to the human (GRCh38) genome using Bowtie2
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 1000 bp windows. The edgeR Pvalue was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR P value less than an arbitrarily chosen threshold were considered DMR. The DMR edges were extended until no genomic window with an edgeR P value less than 0.1 remained within 1000 bp of the DMR.
The selected DMR were then summarized and annotated.
Genome_build: GRCh38
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window and other summary values.

source_name: Buccal

growth_protocol: Two independent single centers (Arthritis Northwest, ANW, Spokane, WA, USA and Dx Biosamples, LLC in San Diego, California, USA) performed the prospective and open clinical study. The participant approval and informed consent was obtained from all participants prior to the clinical sample collection. The study was approved by the Quorum Review Institutional Review Board (IRB) for the ANW Clinic, Spokane, WA with code # AE010831, and Investigational Review Board (www.dxirb.com) of Dx Biosamples, LLC, San Diego, CA, USA, with code IORG # 0006584, and IRB # 00007904. All research was performed in accordance with relevant guidelines/regulations.

extract_protocol:
Buccal samples were frozen and stored (-20 °C) for the subsequent epigenetic analysis. Blood was collected into BD Vacutainer CPT tubes (Becton, Dickinson and Company, Franklin Lakes, NJ) by ANW Spokane, WA and shipped overnight on ice for immediate processing. Monocytes were isolated using antibody-linked magnetic beads (Dynabeads CD14, Life Technologies # 11149D). Human buccal samples were kept frozen and thawed for analysis. Blood samples were kept refrigerated before monocyte isolation. For monocyte isolation the blood was diluted 1:2 in Isolation Buffer (1X PBS, 0.1% BSA, 2mM EDTA) then centrifuged at 600 x g for 10 min at room temperature in a swinging bucket rotor. The plasma upper layer was discarded, and the blood resuspended to the original volume in Isolation Buffer. Magnetic beads (Dynabeads CD14, Life Technologies # 11149D) were added to the blood samples (25 µL of pre-washed beads for 1 ml of blood sample). The mixture (beads-cells) was incubated for 20 min between 2 °C and 8 °C with gentle tilting and rotation. The mixture was then placed on a magnet for 2 minutes and the supernatant carefully removed. One ml of Isolation Buffer was added to the beads-cells mixture then homogenized and incubated 2 minutes on the magnet. This step was repeated at least 3 times. The bead-bound cells were resuspended in 100 µl 1X PBS pH 7.4 and genomic DNA isolation was performed.  Genomic DNA from buccal swabs or monocytes was prepared as follows: The buccal swabs were incubated with 750 µl of cell lysis solution (100 mM NaCl, 10 mM Tris, 25 mM EDTA, 0.5% SDS) and 3.5 µl of Proteinase K (20 mg/ml) for 3 hours in a heating block at 55 °C. The lysis solution was transferred to a new tube and spun for 2 min at full speed. For the monocytes, 820 μl of DNA extraction buffer (50 mM Tris pH 8, 10 mM EDTA pH 8, 0.5% SDS) and 80 μl Proteinase K (20 mg/ml) were added to the bead-bound monocytes and the sample incubated at 55 °C for 2 hours under constant rotation. The samples were placed on a magnet where the magnetic beads were discarded and the supernatants containing the DNA kept. Then for both the buccal swabs and the monocytes, 300 μl of protein precipitation solution (Promega Genomic DNA Purification Kit, A795A, Madison, WI) was added, the sample was mixed and incubated on ice for 15 min, then spun at 4 °C at 13,500 x g for 20 min. The supernatant was transferred to a fresh tube, then precipitated over night at -20 °C with 1 mL of cold 100% isopropanol and 2 μl glycoblue. The sample was then centrifuged at 4 °C, 13,500 x g for 20 min. The supernatant was discarded and the pellet washed with 70% cold ethanol then returned to freezer for 20-30 min. The sample was then centrifuged at 4 °C, 13,500 x g for 10 min. The supernatant was discarded, and the pellet air-dried for 5 min then resuspended in 100 μl nuclease free water. DNA concentration was measured using the Nanodrop (Thermo Fisher, Waltham, MA). Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed as follows: individual genomic DNA samples (2-4 ug of total DNA) were diluted to 130 μl with 1X Tris-EDTA (TE, 10 mM Tris, 1 mM EDTA) and sonicated with the Covaris M220 using the 300 bp setting. Fragment size was verified on a 2% E-gel agarose gel. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube, and the volume was measured. The sonicated DNA was then diluted with TE buffer (10 mM Tris HCl, pH 7.5; 1 mM EDTA) to 400 μl, heat-denatured for 10 min at 95 °C, then immediately cooled on ice for 10 min. Then 100 μl of 5X IP buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4 °C. The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 ml 1X PBS with 0.1% BSA and 2 mM EDTA) was added and the bead sample was resuspended. The tube was then placed into a magnetic rack for 1-2 min and the supernatant was discarded. The tube was removed from the magnetic rack and the beads were washed once. The washed beads were resuspended in the same volume of 1X IP buffer (50 mM sodium phosphate pH 7.0, 700 mM NaCl, 0.25% Triton X-100) as the initial volume of beads. Beads (50 μl) were added to the 500 μl of DNA-antibody mixture from the overnight incubation, then incubated for 2 hours on a rotator at 4 °C. After the incubation, the bead-antibody-DNA complex was washed three times with 1X IP buffer as follows: The tube was placed into a magnetic rack for 1-2 min and the supernatant was discarded, then the magnetic bead antibody pellet was washed with 1X IP buffer 3 times. The washed bead antibody DNA pellet was then resuspended in 250 μl digestion buffer with 3.5 μl Proteinase K (20 mg/ml). The sample was incubated for 2-3 hours on a rotator at 55 °C, then 250 μl of buffered Phenol-Chloroform-Isoamylalcohol solution was added to the sample, and the tube was vortexed for 30 sec and then centrifuged at 14,000 x g for 5 min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250 μl chloroform were added to the supernatant from the previous step, vortexed for 30 sec and centrifuged at 13,500 x g for 5 min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2 μl of glycoblue (20 mg/ml), 20 μl of 5M NaCl and 500 μl ethanol were added and mixed well, then precipitated in -20 °C freezer for 1 hour to overnight. The precipitate was centrifuged at 13,500 x g for 20 min at 4 °C and the supernatant was removed, while not disturbing the pellet. The pellet was washed with 500 μl cold 70% ethanol in -20 °C freezer for 15 min then centrifuged again at 13,500 x g for 5 min at 4 °C and the supernatant was discarded. The tube was spun again briefly to collect residual ethanol to the bottom of the tube and as much liquid as possible was removed with gel loading tip. The pellet was air-dried at RT until it looked dry (about 5 min) then resuspended in 20 μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212).
The MeDIP DNA samples (50 ng of each) were used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra RNA Library Prep Kit for Illumina (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each sample received a separate index primer.

treatment_protocol: The arthritis severity was assessed for the Caucasian population with diagnostic rheumatoid factor autoantibody (RF) positive assay and cyclic citrullinated peptide autoantibody (CCP) positive assay. The arthritis severity was also assessed for both the Caucasian and African American populations with a more qualitative Clinical Disease Activity Index (CDAI) analysis with a high activity score of >22.1-76.0 and moderate activity score of 10.1-22.0. The CDAI was also supported with DAS28 and RAPID3 assays for the Caucasian population.

tag: sample group

value: Rheumatoid arthritis

tag: subject

tag: age


title: AH_32


title: AH_31


title: 150 mM NaCl treated wheat roots rep2


title: AH_30


title: AH_29


title: AH_28


title: AH_26


title: AH_23


title: AH_24


title: AH_25


title: AH_27


title: AH_20


title: AH_19


title: RRBS-PCB126-10nM-Rep1

city: Woods Hole

first: Neelakanteswar

last: Aluru

state: MA

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

data_processing:
DNA methylation analysis was carried out following Bisulfite Analysis Toolkit (BAT). The details are provided in this website: https://www.bioinf.uni-leipzig.de/Software/BAT/. This contains 4 different modules - Mapping,  Calling, Analysis and DMRs
RNAseq - pre-processing using FASTQC
RNAseq - mapping the reads to the genome using STAR
RNAseq - counting the reads using HT-seq count
RNAseq - statistical analysis using edgeR
Genome_build: GRCz10
Supplementary_files_format_and_content: Text format; RNAseq data files (Htseq-count) contains read counts. DMR data contains statistically significant DMRs and statistical data.
Supplementary_files_format_and_content: P0_3.metilene_qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO
Supplementary_files_format_and_content: P10.metilene_qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO
Supplementary_files_format_and_content: P0_3-overlap-P10.txt: Common DMRs between 3 and 10nM PCB126 groups

organism: Danio rerio

source_name: testis

extract_protocol:
Total RNA and DNA were isolated using the ZR-Duet™ DNA/RNA Mini Prep kit (Zymo Research, CA).
Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single-ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT-Dx, a Diagenode company (Ghent, Belgium). Briefly, libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI (New England Biolabs, MA), followed by end repair and A-tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor-ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end (PE) sequencing was performed on an Illumina HiSeq2500 platform.

treatment_protocol: Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant-free water for 7 days prior to sampling the testis tissue.

value: testis

value: Adult


title: RRBS-PCB126-10nM-Rep2


title: RRBS-PCB126-3nM-Rep5


title: RRBS-PCB126-10nM-Rep4


title: RRBS-PCB126-10nM-Rep3


title: RRBS-PCB126-3nM-Rep4


title: AH_18


title: Non-axenic larvae rep1 [na.lar1]

value: Non-axenic/control

value: L4 Larvae


title: RRBS-PCB126-3nM-Rep6


title: RRBS-PCB126-3nM-Rep3


title: RRBS-PCB126-3nM-Rep2


title: AH_17


title: RRBS-PCB126-3nM-Rep1


title: AH_16


title: RRBS-PCB126-10nM-Rep5


title: RRBS-DMSO-Rep1

value: DMSO


title: RRBS-DMSO-Rep4


title: RRBS-DMSO-Rep5


title: RRBS-DMSO-Rep2


title: RRBS-DMSO-Rep3


title: GBM Patient [ndGBM-02-5]

source_name: Human Tumor Tissue

tag: subject status

value: GBM Patient

tag: tumor grade

value: IV

tag: Sex

value: Male


title: AH_15

value: Control


title: GBM Patient [ndGBM-02-1]


title: AH_13


title: GBM Patient [ndGBM-02-2]


title: GBM Patient [ndGBM-02-4]


title: GBM Patient [ndGBM-11-C]

value: II

value: Female


title: GBM Patient [ndGBM-11-B]


title: GBM Patient [ndGBM-11-D]


title: nANW16

description: anw.buccal.results.csv.gz, comb.buccal.results.csv.gz

value: ANW C13


title: AH_10


title: GBM Patient [ndGBM-11-A]


title: H37Rv_T72_RIF_0.02_C

first: Eliza

last: Peterson

address: 401 Terry Ave N

institute: Institute for Systems Biology

data_processing:
Illumina RiboZero bacteria kit was used for rRNA depletion. Samples were sequenced on the NextSeq sequencing instrumetn in mid output 150 v2 flow cell. Paired-end 75 bp reads were checked for technical artifacts using FastQC following Illumina default quality filtering steps. Raw FASTQ read data were processed using the R package DuffyNGS.
Genome_build: Mycobacterium tuberculosis H37Rv ASM19595v2
Supplementary_files_format_and_content: tab-delimited text file includes RPKM and read counts for each sample

organism: Mycobacterium tuberculosis

source_name: H37Rv_T72_RIF_0.02_bacterial culture

growth_protocol: Samples grown in 7H9-rich media  at 37 degrees C with shaking

extract_protocol:
In three biological replicates, M. tuberculosis cultures with or without drug treatment were harvested at 4, 24  or 72 h. Cells pellets were spun down and immediately frozen in liquid nitrogen and stored at -80 degrees C until RNA isolation. Cell pellets were transferred to a tube containing Lysing Matrix B, and vigorously shaken at max speed for 30 s in a FastPrep 120 homogenizer three times. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a fresh tube. RNA was isolated using phenol-chloroform extraction method, followed by DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treatment with no drug or Rifampicin at 0.008 or 0.02 μg/mL for 4, 24 or 72 h

tag: strain

tag: drug treatment

tag: treatment time

value: 72 hour


title: H37Rv_T72_RIF_0.02_A


title: H37Rv_T24_RIF_0.02_A

source_name: H37Rv_T24_RIF_0.02_bacterial culture

value: 24 hour


title: nANW15

value: ANW C12


title: H37Rv_T24_RIF_0.02_C


title: H37Rv_T72_RIF_0.02_B


title: nANW13

value: ANW C10


title: nANW14

value: ANW C11


title: H37Rv_T4_RIF_0.02_C

source_name: H37Rv_T4_RIF_0.02_bacterial culture

value: 4 hour


title: H37Rv_T24_RIF_0.02_B


title: H37Rv_T4_RIF_0.02_B


title: AH_22

value: Rheumatoid arthritis


title: AH_12


title: H37Rv_T4_RIF_0.02_A


title: nANW11

value: ANW T16


title: H37Rv_T72_RIF_0.008_C

source_name: H37Rv_T72_RIF_0.008_bacterial culture


title: nANW12

value: ANW T17


title: H37Rv_T72_RIF_0.008_A


title: nANW10

value: ANW T15


title: H37Rv_T24_RIF_0.008_C

source_name: H37Rv_T24_RIF_0.008_bacterial culture


title: H37Rv_T24_RIF_0.008_B


title: H37Rv_T72_RIF_0.008_B


title: nANW9

value: ANW T14


title: H37Rv_T4_RIF_0.008_C

source_name: H37Rv_T4_RIF_0.008_bacterial culture


title: H37Rv_T24_RIF_0.008_A


title: nANW8

description: monocyte.results.csv.gz

source_name: Monocyte


title: H37Rv_T4_RIF_0.008_B


title: H37Rv_T4_RIF_0.008_A


title: nANW7

description: monocyte.results.csv.gz


title: AH_14


title: H37Rv_T72_RIF_0x_E

source_name: H37Rv_T72_RIF_0x_bacterial culture

value: no drug


title: H37Rv_T72_RIF_0x_F


title: nANW6

description: monocyte.results.csv.gz


title: H37Rv_T72_RIF_0x_D


title: H37Rv_T24_RIF_0x_D

source_name: H37Rv_T24_RIF_0x_bacterial culture


title: nANW4

description: monocyte.results.csv.gz


title: H37Rv_T4_RIF_0x_F

source_name: H37Rv_T4_RIF_0x_bacterial culture


title: H37Rv_T4_RIF_0x_E


title: H37Rv_T4_RIF_0x_D


title: nANW3

description: monocyte.results.csv.gz


title: H37Rv_T72_BDQ_11.5_C

source_name: bacterial culture

treatment_protocol: Treatment with no drug or Bedaquiline at 5.75 or 11.5 μg/mL for 4, 24 or 72 h


title: nANW2

description: monocyte.results.csv.gz


title: H37Rv_T72_BDQ_11.5_A


title: 57C_Malignant melanoma of the skin

description: Hybridized to CytoScan HD

source_name: Malignant melanoma tissue, cryopreserved, autopsy

tag: cell type

value: malignant melanoma


title: nANW1

description: monocyte.results.csv.gz


title: H37Rv_T24_BDQ_11.5_C


title: H37Rv_T24_BDQ_11.5_B


title: H37Rv_T72_BDQ_11.5_B


title: H37Rv_T24_BDQ_11.5_A


title: ANW35

value: Control

value: ANW C08


title: ANW36

value: ANW C09


title: 19G_Malignant melanoma of the skin

description: Hybridized to CytoScan HD


title: 19H_Malignant melanoma of the skin

description: Hybridized to CytoScan HD


title: H37Rv_T4_BDQ_11.5_A


title: 55C_Malignant melanoma of the skin

description: Hybridized to CytoScan HD


title: 20C_Malignant melanoma of the skin

description: Hybridized to CytoScan HD


title: 56C_Malignant melanoma of the skin

description: Hybridized to CytoScan HD


title: H37Rv_T4_BDQ_11.5_B


title: nANW5

description: monocyte.results.csv.gz


title: H37Rv_T72_BDQ_5.75_C


title: 54F_Malignant melanoma of the skin

description: Hybridized to CytoScan HD


title: 31C_Malignant melanoma of the skin

description: Hybridized to CytoScan HD


title: H37Rv_T72_BDQ_5.75_B


title: H37Rv_T72_BDQ_5.75_A


title: 36C2_Malignant melanoma of the skin

description: Hybridized to CytoScan HD


title: 17B_Malignant melanoma of the skin

description: Hybridized to CytoScan HD


title: 17C_Malignant melanoma of the skin

description: Hybridized to CytoScan HD


title: ANW33

value: ANW C06


title: 57B1_Malignant melanoma of the skin

description: Hybridized to CytoScan HD


title: H37Rv_T24_BDQ_5.75_B


title: 55B_Malignant melanoma of the skin

description: Hybridized to CytoScan HD


title: H37Rv_T24_BDQ_5.75_A


title: ANW31

value: ANW C04


title: H37Rv_T4_BDQ_5.75_C


title: H37Rv_T72_BDQ_0x_C

value: 72 hour


title: 31A_Malignant melanoma of the skin

description: Hybridized to CytoScan HD


title: H37Rv_T24_RIF_0x_F

value: 24 hour


title: 56B_Malignant melanoma of the skin

description: Hybridized to CytoScan HD


title: H37Rv_T72_BDQ_0x_B


title: ANW32

value: ANW C05


title: H37Rv_T24_BDQ_5.75_C


title: ANW30

value: ANW C03


title: H37Rv_T24_BDQ_0x_C


title: ANW29

value: ANW C02


title: H37Rv_T24_BDQ_0x_A


title: H37Rv_T4_BDQ_0x_C

value: 4 hour


title: ANW27

value: Rheumatoid arthritis

value: ANW T13


title: ANW28

value: ANW C01


title: H37Rv_T4_BDQ_5.75_B


title: H37Rv_T4_BDQ_0x_B


title: H37Rv_T4_BDQ_0x_A


title: H37Rv_T24_BDQ_0x_B


title: H37Rv_T4_BDQ_5.75_A


title: H37Rv_T72_BDQ_0x_A


title: ANW25

value: ANW T10


title: H37Rv_T72_MXF_0.3_C

treatment_protocol: Treatment with no drug or Moxifloxacin at 0.12 or 0.3 μg/mL for 4, 24 or 72 h

value: 0.3 ug/mL


title: H37Rv_T24_RIF_0x_E

value: no drug


title: H37Rv_T72_MXF_0.3_A


title: ANW24

value: ANW T09


title: H37Rv_T24_MXF_0.3_C


title: H37Rv_T72_MXF_0.3_B


title: H37Rv_T24_MXF_0.3_B


title: H37Rv_T4_MXF_0.3_C


title: ANW26

value: ANW T12


title: ANW22

value: ANW T05


title: 57I_Malignant melanoma of the skin

description: Hybridized to CytoScan HD

value: malignant melanoma


title: H37Rv_T4_MXF_0.3_A


title: H37Rv_T72_MXF_0.12_C


title: ANW20

value: ANW T03


title: H37Rv_T72_MXF_0.12_A

value: 72 hour


title: ANW19

value: ANW T01


title: H37Rv_T72_MXF_0.12_B


title: H37Rv_T24_MXF_0.12_C

value: 24 hour


title: H37Rv_T24_MXF_0.12_B


title: ANW18

description: monocyte.results.csv.gz

value: Control

value: ANW C09


title: H37Rv_T4_MXF_0.12_C

value: 4 hour


title: H37Rv_T4_MXF_0.12_B


title: ANW17

description: monocyte.results.csv.gz

value: ANW C08


title: H37Rv_T4_MXF_0.12_A


title: ANW21

value: Rheumatoid arthritis

value: ANW T04


title: ANW16

description: monocyte.results.csv.gz

value: ANW C07


title: H37Rv_T24_MXF_0x_C


title: H37Rv_T24_MXF_0x_A


title: H37Rv_T24_MXF_0x_B


title: H37Rv_T72_MXF_0x_A


title: ANW13

description: monocyte.results.csv.gz

value: ANW C04


title: ANW14

description: monocyte.results.csv.gz

value: ANW C05


title: H37Rv_T4_MXF_0.3_B

value: 0.3 ug/mL


title: ANW11

description: monocyte.results.csv.gz

value: ANW C02


title: H37Rv_T24_MXF_0.12_A


title: H37Rv_T4_BDQ_11.5_C


title: H37Rv_T4_MXF_0x_B

value: no drug


title: H37Rv_T4_MXF_0x_C


title: H37Rv_T4_MXF_0x_A


title: H37Rv_T72_MXF_0x_C


title: ANW15

description: monocyte.results.csv.gz

value: ANW C06


title: ANW10

description: monocyte.results.csv.gz

value: ANW C01