title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL017923_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB017946_G1]

status: Public on Mar 09 2022

type: genomic

city: Memphis

first: Zhaoming

last: Wang

state: TN

address: 262 Danny Thomas Place

department: Epidemiology & Cancer Control

country: USA

institute: St. Jude Children's Research Hospital

description: blood from survivor of childhood cancer

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium MethylationEPIC BeadChips using standard Illumina protocal

scan_protocol: Arrays were stained and scanned using the Illumina HiScan system with standard recommended Illumina scanner setting

data_processing:
GenomeStudio V2011.1
Average Beta
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood mononuclear cells

label_protocol: Standard Illumina Protocal

extract_protocol: DNA extracted from periperihal blood mononuclear cells using the QIAamp DNA Blood Mini Kit (Qiagen cat#51106)

tag: gender

value: Female

tag: age

tag: anthracyclines

tag: alkylating agent,classic

tag: corticosteroids

tag: epipodophyllotoxins

tag: vincristine

tag: platinum

tag: brainrt

tag: chestrt


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018544_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW37_14

type: SRA

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

description:
singlecell_countmatrix.tsv.gz
singlecell_metadata.tsv

library_source: transcriptomic

data_processing:
Single cell only: The 4bp UMI sequence (initially sequenced in read1), are appended at the end of the headers of the reads (here the reads we provide are resulting from this operation)
Reads are mapped with STAR on the mouse genome GRCm38 considering Ensembl 85 as genome annoatations
Single cell only: bam files are processed with umi_tools to deduplicate reads with identical UMI sequence
gene expression are quantifyied using summarizeOverlaps() method of the R package GenomicsAlignments(). Only exonic reads are considered in the quantification (this includes 5' and 3' UTRs), and only reads with a mapping quality >=255 (to exclude those ambiguously mapping at multiple positions).
Genome_build: GRCm38
Supplementary_files_format_and_content: singlecell_countmatrix.tsv.gz: is a count matrix in tab-separated format. It contains the result of the single cell quantification for all genes. The integers values represent the number of exonic reads mapping into each gene after UMI correction. The first columns contains the gene name that is quantified.    bulk_countmatrix.tsv.gz: count matrix for the bulk experiments in tab-separated format.    singlecell_metadata.tsv: is a table containing metadata information for each cell in tab-separated. The content of the columns are: MT=proportion of mithocondrial reads; ngenes=number of expressed gene; epor_age=age at which the mous as been electroporated; collection_age=age at which cells were collected; cond=condition Control/miR-137/miR-122; cell_type, cell_type_pred1, cell_type_pred2: predicted cell types for the cell; tSNE1, tSNE2= coordinate of the cell in the t-SNE space

molecule: polyA RNA

organism: Mus musculus

source_name: cortex

extract_protocol:
Single-cell RNA sequencing    Embryonic cortex: Tissue collection was performed as in Telley et al., Science 2019. Briefly, pregnant females were sacrificed, and embryos were extracted in ice-cold HBSS either at E15.5 and E17.5 after E14.5 in utero electroporation. Three hundred micrometer- acute coronal brain sections were performed after embedding in 4% low melt- agar using a vibratome (Leica, #VT1000S) under RNase-free conditions. The putative primary somatosensory cortex (S1) was microdissected using a Leica Dissecting Microscope (Leica, #M165FC) and incubated in 0.05% trypsin at 37°C for 5 minutes. Following tissue digestion, cells were incubated in fetal bovine serum and cells were manually dissociated via gentle pipetting. Cells were then centrifuged for 5 minutes at 500 rpm, resuspended in 1 mL FACS buffer (2 mg/mL glucose, 0.1% bovine serum albumin, 1/50 citrate phosphate dextrose, 10 units/mL DNaseI, 1 uM MgCl2, in L15 medium) and filtered using a 70 mm- cell strainer (ClearLine, #141379C), before 10 minute- incubation with Hoechst (0.1 mg/mL) at 37°C .    Postnatal cortex: Tissue collection was performed as in Klingler et al., Curr Biol 2019. Briefly, 600 um acute coronal brain sections were cut on a vibratome and S1 was microdissected as described above in ice-cold oxygenated artificial cerebrospinal fluid (ACSF) under RNase-free conditions. Cells were next dissociated by incubating microdissected samples in 0.5 mg/mL pronase (Sigma, #P5147) at 37°C for 10 minutes, followed by a 3 minute- inactivation in 5% bovine serum albumin, washes in ACSF and manual trituration using pulled glass pipettes of decreasing diameters. Cells were then centrifuged for 10 minutes at 500 rpm, resuspended and filtered using a 70 um- cell strainer (ClearLine, #141379C), incubated for 10 minutes with Hoechst (0.1 mg/mL) at 37°C.    Singlet GFP+/Hoechst+ embryonic and postnatal cells were sorted using a Beckman Coulter Moflo Astrios FAC-sorter according to their Forward and Slide scattering properties, and their negativity for Draq7TM (Viability dye, far red DNA intercalating agent, Beckman Coulter, #B25595). Three microliters of C1 Suspension Reagent (Fluidigm) was added to 10 ul of FACsorted cells, which were captured into 800 well- AutoPrep integrated fluidic circuit (IFC) designed for 10 to 17 um diameter-cells (Fluidigm HT800, #100-57-80), and imaged using the ImageXpress Micro Widefield High Content Screening System (Molecular Devices®).        Bulk RNA sequencing    Brains were collected from E14.5 in utero electroporated miR-122 pups at P7. The primary somatosensory cortex was microdissected following the same procedure as described above with further separation of superficial (SL) and deep (DL) layers. SL and DL cells were dissociated and FACsorted as for single-cell RNA sequencing.
Single-cell RNA sequencing  cDNA synthesis and preamplification was processed following the manufacturer’s instructions (C1 system, Fluidigm). cDNA libraries were prepared using Nextera XT DNA library prep kit (Illumina), quality control was done using 2001 Bioanalyzer from Agilent, and sequenced using HiSeq 2500 sequencer for E14.5 electroporated pups, and HiSeq 5000 sequencer for E14 and E15.5 electroporated pups with an expected sequencing depth of 1M reads per single cell, and a final mapping read length of 70bp.    Bulk RNA sequencing  RNA from each sample was extracted and quality control was done using 2001 Bioanalyzer from Agilent. cDNA libraries were obtained using SMARTseq v4 kit (Clontech, # 634888) and sequenced using HiSeq 2500 sequencer.

tag: tissue

value: cortex


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM017957_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM017962_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW37_20


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM017963_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW36_4


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS017898_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW36_16


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL017881_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW37_18


title: UTHT1_ROW36_20


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL017918_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW37_8


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018504_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL017907_G1]

description: blood from survivor of childhood cancer

value: Male


title: UTHT1_ROW37_2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB017939_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018515_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL017904_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW37_1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM017960_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW37_12


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL017926_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL017929_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW35_4


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB018831_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018911_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL003458_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW35_12


title: UTHT1_ROW35_13


title: UTHT1_ROW37_16


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM017961_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW36_14


title: UTHT1_ROW36_13


title: UTHT1_ROW36_1


title: UTHT1_ROW35_19


title: UTHT1_ROW36_9


title: UTHT1_ROW34_3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM017955_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041929_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW34_2


title: UTHT1_ROW35_7


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041894_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL017922_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCA017893_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW35_1


title: UTHT1_ROW34_13


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS042704_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL017917_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW33_8


title: UTHT1_ROW33_3


title: UTHT1_ROW33_2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042696_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS017952_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041935_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW35_6


title: UTHT1_ROW35_10


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS042714_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW34_15


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042662_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW34_1


title: UTHT1_ROW33_17


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS042766_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW33_15


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041942_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW34_8


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042744_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042086_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB041689_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW35_14


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL043130_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041030_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW32_8


title: UTHT1_ROW32_7


title: UTHT1_ROW33_10


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT042716_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW32_4


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL005343_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW33_14


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042689_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW32_19


title: UTHT1_ROW33_12


title: UTHT1_ROW35_18


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB042765_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW33_13


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB042497_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041856_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042653_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW31_4


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS042496_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041891_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW31_17


title: UTHT1_ROW32_18


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS042105_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM019655_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW32_2


title: UTHT1_ROW33_11


title: UTHT1_ROW31_5


title: UTHT1_ROW30_9


title: UTHT1_ROW32_17


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT042487_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041908_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041979_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041022_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004196_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW31_6


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041851_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW31_13


title: UTHT1_ROW31_19


title: UTHT1_ROW33_19


title: UTHT1_ROW30_20


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041198_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB042761_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW31_1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS042486_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW30_7


title: UTHT1_ROW31_7


title: UTHT1_ROW34_18


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS042127_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW30_13


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL040973_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW30_2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041963_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW30_11


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041002_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW30_17


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS040991_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW30_12


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041236_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042652_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW29_9


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041970_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042064_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW29_7


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS042100_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041958_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW29_6


title: UTHT1_ROW29_5


title: UTHT1_ROW29_2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041292_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW29_19


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL041039_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW29_17


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042026_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL005347_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW29_16


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL042004_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW29_14


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042618_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW29_13


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS041986_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW30_10


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041461_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW29_12


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041208_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019306_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW29_10


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041944_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041972_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS042096_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW28_5


title: UTHT1_ROW28_20


title: UTHT1_ROW28_4


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041254_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW28_16


title: UTHT1_ROW28_15


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018944_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041435_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW28_14


title: UTHT1_ROW28_10


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041953_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS001304_G2]

description: blood from survivor of childhood cancer


title: UTHT1_ROW28_12


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL042539_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB042115_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW27_9


title: UTHT1_ROW27_4


title: UTHT1_ROW27_6


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041455_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018957_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW27_7


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041229_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW27_2


title: UTHT1_ROW27_20


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041918_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS042109_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW27_19


title: UTHT1_ROW28_2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHIST042002_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018985_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW27_18


title: UTHT1_ROW27_16


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041257_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW27_15


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL019468_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW26_9


title: UTHT1_ROW26_7


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041971_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041873_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW26_4


title: UTHT1_ROW26_3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019044_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW26_18


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042087_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041875_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW26_19


title: UTHT1_ROW26_17


title: UTHT1_ROW26_11


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS041917_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041186_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL042080_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL041325_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM041025_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW25_20


title: UTHT1_ROW25_15


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS019602_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW25_12


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018987_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJST042112_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019128_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW25_1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL019486_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW24_8


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019049_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019069_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019348_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW24_6


title: UTHT1_ROW24_17


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS019512_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018982_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW24_16


title: UTHT1_ROW25_6


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL019496_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW24_13


title: UTHT1_ROW24_14


title: UTHT1_ROW23_4


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018974_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW25_13


title: UTHT1_ROW23_17


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019305_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS019604_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL019473_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019131_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW23_13


title: UTHT1_ROW23_14


title: UTHT1_ROW25_10


title: UTHT1_ROW23_12


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL019430_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML018553_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW22_2


title: UTHT1_ROW22_20


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB019587_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW24_7


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019134_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW22_14


title: UTHT1_ROW27_17


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018943_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW22_13


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018420_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW22_12


title: UTHT1_ROW22_10


title: UTHT1_ROW21_6


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019263_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019150_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW21_20


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019250_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019056_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM019641_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW22_16


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS001207_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW21_14


title: UTHT1_ROW21_1


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018668_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018510_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML019107_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW20_19


title: UTHT1_ROW21_11


title: UTHT1_ROW20_3


title: UTHT1_ROW20_17


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019359_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019329_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018941_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS001204_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW20_10


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHIST019244_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW20_14


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL019456_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW19_10


title: UTHT1_ROW19_4


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL006047_G2]

description: blood from survivor of childhood cancer


title: UTHT1_ROW19_9


title: UTHT1_ROW18_3


title: UTHT1_ROW18_6


title: UTHT1_ROW18_20


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018952_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW21_13


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019017_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW18_18


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019175_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW18_15


title: UTHT1_ROW18_14


title: UTHT1_ROW18_10


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018680_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019123_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW17_6


title: UTHT1_ROW17_9


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM019645_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019168_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW17_4


title: UTHT1_ROW17_20


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS019517_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW17_19


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018507_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018418_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHIST018641_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW17_17


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL019428_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW17_14


title: UTHT1_ROW17_12


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018939_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS001218_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019271_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW16_2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL019408_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019247_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW16_4


title: UTHT1_ROW16_19


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGICT018824_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS018862_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL018757_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019135_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW16_10


title: UTHT1_ROW15_9


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS019206_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018699_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW16_15


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJMEL019375_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL019472_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW15_13


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018963_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB003947_G2]

description: blood from survivor of childhood cancer


title: UTHT1_ROW17_18


title: UTHT1_ROW22_15


title: UTHT1_ROW16_16


title: UTHT1_ROW14_9


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM019654_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW14_20


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019180_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML019105_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019186_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW15_15


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018893_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW16_12


title: UTHT1_ROW15_3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM019637_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW14_12


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS018614_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018934_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS019509_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM019652_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW14_3


title: UTHT1_ROW14_6


title: UTHT1_ROW14_15


title: UTHT1_ROW13_20


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL019466_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS018590_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018902_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW14_10


title: UTHT1_ROW16_14


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018948_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW14_2


title: UTHT1_ROW13_5


title: UTHT1_ROW14_11


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019009_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL018775_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL018777_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW13_6


title: UTHT1_ROW13_11


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL019497_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018657_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB018847_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW13_17


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL018780_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW12_15


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB019583_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW12_14


title: UTHT1_ROW12_13


title: UTHT1_ROW12_11


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018899_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS019519_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW13_19


title: UTHT1_ROW12_1


title: UTHT1_ROW12_2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS018607_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW12_8


title: UTHT1_ROW12_19


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019739_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019751_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018670_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW11_19


title: UTHT1_ROW13_12


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB018829_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW12_10


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS018620_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW11_16


title: UTHT1_ROW11_20


title: UTHT1_ROW11_4


title: UTHT1_ROW11_14


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018650_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019734_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS018583_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW13_15


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018523_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW12_16


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL018753_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW11_11


title: UTHT1_ROW11_12


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018707_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW12_4


title: UTHT1_ROW11_2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018687_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW11_17


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018516_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018892_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018879_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018530_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS019614_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNBL019405_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW11_13


title: UTHT1_ROW10_2


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL018766_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW10_18


title: UTHT1_ROW10_9


title: UTHT1_ROW10_7


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHIST018643_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW10_6


title: UTHT1_ROW10_15


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS019760_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB018840_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW10_13


title: UTHT1_ROW10_10


title: UTHT1_ROW10_5


title: UTHT1_ROW09_8


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS018870_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018877_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB019580_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW10_11


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018679_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL017887_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW09_19


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL004739_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018438_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019034_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW09_13


title: UTHT1_ROW08_7


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018673_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM018875_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM019668_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS018618_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL019321_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW08_3


title: UTHT1_ROW08_8


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJMEL019799_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW08_20


title: UTHT1_ROW08_2


title: UTHT1_ROW09_6


title: UTHT1_ROW08_19


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018439_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW08_17


title: UTHT1_ROW08_18


title: UTHT1_ROW08_16


title: UTHT1_ROW08_15


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019051_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW08_13


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018953_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW09_12


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJOS017934_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL019750_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW08_12


title: UTHT1_ROW08_6


title: UTHT1_ROW08_10


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018479_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW07_5


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018473_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL017931_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW07_3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018935_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS018596_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJEWS018622_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT019237_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS018565_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS010133_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW07_19


title: UTHT1_ROW07_14


title: UTHT1_ROW07_11


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018405_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW07_20


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM017959_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW07_17


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS018584_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW06_7


title: UTHT1_ROW07_10


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018433_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS018574_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW06_4


title: UTHT1_ROW06_15


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS019623_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018409_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJWLM017958_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW06_14


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJHL018648_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW06_13


title: UTHT1_ROW06_12


title: UTHT1_ROW05_9


title: UTHT1_ROW05_4


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJCNS018598_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRHB019598_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJAML018554_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJRB018826_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJGCT019231_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW05_20


title: UTHT1_ROW05_19


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018469_G1]

description: blood from survivor of childhood cancer


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL017927_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW05_18


title: UTHT1_ROW05_13


title: UTHT1_ROW05_15


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJNHL017924_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW04_7


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJSTS018869_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW05_5


title: UTHT1_ROW04_15


title: UTHT1_ROW05_10


title: UTHT1_ROW04_9


title: UTHT1_ROW05_3


title: genomic DNA derived from blood samples from survivor of childhood cancer [SJALL018498_G1]

description: blood from survivor of childhood cancer


title: UTHT1_ROW04_2


title: Vero_NSP8 rep2 input

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description:
eCLIP8_1.Vero_NSP8-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP8_1.Vero_NSP8-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

data_processing:
Sequenced reads were reformatted to include randomers in read headers with umi_tools (1.0.0). Args: --random-seed 1 --bc-pattern NNNNNNNNNN
Reads were then trimmed with cutadapt (1.14). Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -a InvRNA*.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
Reads were then trimmed once more with cutadapt (1.14) to remove double-ligation events. Args: --match-read-wildcards -O 5 --times 1 -e 0.1 --quality-cutoff 6 -m 18  -a InvRNA*.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
Trimmed reads were then mapped with STAR (2.4.0i) against a repeat element database (RepBase 18.05). Args: --runThreadN 16 \  --genomeDir human_repbase \  --readFilesIn path/to/read1 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 30 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Unmapped reads filtered of repeat elements were then mapped with STAR (2.4.0i) against a human genome (hg19/ChlSab2). Args: --runThreadN 16 \  --genomeDir genomedir \  --readFilesIn /path/to/read1 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM   Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 1 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Aligned reads were sorted with samtools (1.6)
Sorted reads were collapsed with umi_tools (1.0.0). Args: --random-seed 1 --method unique
BAM files were used to identify peak clusters with Clipper (1.2.2). Args: --species (hg19/ChlSab2_Sars) --bam path/to/input.bam --timeout 3600000 --maxgenes 1000000 --save-pickle --outfile path/to/output.bam
Peak clusters were normalized using BAM files for IP against BAM files for INPUT with peaksnormalize.pl (overlap_peakfi_with_bam_PE.pl), included in eclip 0.1.5+.
Overlapping normalized peak regions were merged with compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl, included within eclip-0.1.5+
Normalized peak (compressed.bed) files were ranked by entropy score (make_informationcontent_from_peaks.pl included within the merge_peaks pipeline) and used as inputs to IDR (2.0.2) to determine reproducible peaks.
Reproducible peaks were filtered for those ≥20 bases in length, and not overlapping with WT negative control samples.
Genome_build: hg19
Genome_build: ChlSab2
Genome_build: Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome (MN908947.3)

molecule: total RNA

organism: Chlorocebus sabaeus

source_name: Vero E6 cells infected with SARS-CoV-2

growth_protocol:
BEAS-2B cells were cultured on Matrigel (Corning) coated plates and maintained in the PneumaCult-Ex Plus Medium (Stem Cell Technologies), supplemented with 33 µg/ml hydrocortisone (Stem Cell Technologies). Growth media was replaced every two days, and the cells were passaged every four days. Vero E6 cells were cultured in DMEM (ThermoFisher) supplemented with 10% FBS (ThermoFisher) and passaged every three days. All cell cultures were incubated at 37ºC and 5% CO2.
Vero E6 cells were cultured in DMEM supplemented with 10% FBS.

extract_protocol:
Biological replicates (according to ENCODE requirements) of 20 million cells were treated with 400mJ of UV using the Stratalinker 2400, harvested by scraping in ice cold PBS and pellets flash frozen in liquid nitrogen and stored in -80 degrees until ready to IP with antibody bound Dynabeads Subsequent protocol exactly as detailed in Van Nostrand et al 2016. Sequencing was performed on Illumina 2000 Hi Seq paired end reads and data processed through Dr. Yeo's eCLIP pipeline.
Libraries were constructed as per the eCLIP protocol using Illumina 50x forward and 70x reverse primers.
eCLIP

treatment_protocol:
Cells were UV cross-linked with 400 mJ/cm^2 and processed through the eCLIP protocol as previously described (van Nostrand et al, 2016). Anti-Strep tag or Anti-FLAG tag antibody was  employed for immunoprecipitation.
Vero E6 cells were infected with SARS-CoV-2 at MOI of 0.02 for 48 hours before UV crosslinking with 400 mJ/cm^2. Anti-N, Anti-NSP8 and Anti-NSP12 antibodies were used for immunoprecipitation.

tag: antibody manufacturer

value: GeneTex

tag: antibody catalog #

value: SARS-CoV / SARS-CoV-2 (COVID-19) NSP8 antibody [5A10] (Mouse), GeneTex, Cat. no. GTX632696

tag: antibody

tag: adapter


title: Vero_NSP8 rep1 input

description:
eCLIP8_1.Vero_NSP8-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP8_1.Vero_NSP8-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: Vero_NSP12 rep1 input

description:
eCLIP8_1.Vero_NSP12-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP8_1.Vero_NSP12-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

value: SARS-CoV-2 (COVID-19) RdRp (nsp12) antibody (Rabbit), GeneTex, Cat. no. GTX135467


title: UTHT1_ROW04_13


title: Vero_N rep2 input

description:
eCLIP8_1.Vero_N-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP8_1.Vero_N-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw

value: Sino Biological

value: SARS-CoV-2 (2019-nCoV) Nucleocapsid Antibody (Rabbit), Sino Biological, Cat. no. 40143-R019


title: UTHT1_ROW04_11


title: Vero_N rep1 input

description:
eCLIP8_1.Vero_N-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP8_1.Vero_N-1-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: UTHT1_ROW03_9


title: UTHT1_ROW03_8


title: UTHT1_ROW03_4


title: Vero_NSP8 rep2 IP


title: Vero_NSP12 rep1 IP


title: Vero_N rep1 IP


title: UTHT1_ROW03_7


title: UTHT1_ROW03_13


title: Vero_NSP8 rep1 IP


title: Vero_NSP12 rep2 input

description:
eCLIP8_1.Vero_NSP12-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw
eCLIP8_1.Vero_NSP12-2-IN.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw


title: ID152

city: London

first: Robin

last: Mesnage

address: Guy's Hospital, 8th Floor, Tower Wing

country: United Kingdom

institute: Kings College London

description: GC.RM.9222.BT5011.152.F.215498_S48_L001_R1_001

data_processing:
Analysis of small RNA sequencing data was performed with miRge3.0. This was done in a Conda environment on a Linux machine using the command line version of miRge3.0. We took into account UMIs in order to remove PCR duplicates and used standard small RNA libraries as a reference. The output of miRge3.0 was then imported in R (v4.0.0) for statistical analysis.
Genome_build: MiRge3.0 catalogue
Supplementary_files_format_and_content: umi count data

organism: Rattus norvegicus

source_name: Pesticide Mixture_liver

growth_protocol: The animal study was performed on young adult female Sprague-Dawley rats at the Cesare Maltoni Cancer Research Center, Ramazzini Institute (Bentivoglio, Italy), in accordance with Italian law regulating the use and humane treatment of animals for scientific purposes (Decreto legislativo N. 26, 2014. Attuazione della direttiva n. 2010/63/UE in materia di protezione degli animali utilizzati a fini scientifici. - G.U. Serie Generale, n. 61 del 14 Marzo 2014). The experiment was authorised by the ad hoc commission of the Italian Ministry of Health (authorization N. 447/2018-PR)

extract_protocol:
RNA was extracted from rat liver tissue excised at the time of sacrifice and which had been stored at -70°C, using the All Prep DNA/RNA/miRNA Universal Kit (Qiagen, Hilden, Germany) using the manufacturer’s instructions. Tissue weight used was ≤ 30 mg, and samples were eluted in 30µl RNase-Free Water. RNA samples were quantified with the Nanodrop 8000 spectrophotometer V2.0 (ThermoScientific, USA) and integrity were checked using the Agilent 2100 Bioanalyser (Agilent Technologies, Waldbronn, Germany). All samples had RNA integrity numbers (RIN) ≥ 7.
We created miRNA libraries from 100 ng total RNA using the QIAseq miRNA library kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions. This kit was chosen to incorporate unique molecular indices (UMIs) into each cDNA to enable correction for PCR bias. Library concentrations were measured using Qubit™ dsDNA HS Assay Kit (Thermo Fisher, USA). Size of the libraries and calculation of the final molarity for pooling the libraries for sequencing was performed with the High Sensitivity D1000 ScreenTape Assay on a Agilent 2200 TapeStation System (Agilent Technologies, Waldbronn, Germany). Average sizes of the fragments were 181 ± 22 bp, with TapeStation molarity of of 31.8 ± 12.9 nM.
Libraries were normalised to 3nM before pooling for sequencing. All samples and all libraries were of good quality and 75 bp single reads were generated for each library using the Illumina NextSeq®500 v2.5 High-output 150 cycle kit (Illumina Inc., Cambridge, UK). A total of 111,746,220 reads were generated for these 24 samples (4,656,093 ± 2,282,243 reads per sample).

treatment_protocol: In brief, groups of 12 female Sprague-Dawley rats of 8 weeks of age were treated for 90 days with a mixture of glyphosate (0.5 mg/kg bw/day), azoxystrobin (0.2 mg/kg bw/day), boscalid (0.04 mg/kg bw/day), chlorpyrifos (0.001 mg/kg bw/day), imidacloprid (0.06 mg/kg bw/day), and thiabenzadole (0.1 mg/kg bw/day) via drinking water, and glyphosate (G50) (50 mg/kg bw/day), or its representative EU commercial herbicide formulation Roundup MON 52276 (R50) at the same glyphosate equivalent doses in comparison to a control group (CON).

tag: group

value: MIX

tag: strain

value: Sprague-Dawley

value: Liver


title: UTHT1_ROW03_20


title: UTHT1_ROW03_14


title: Vero_N rep2 IP


title: UTHT1_ROW03_12


title: ID148

description: GC.RM.9222.BT5011.148.F.215416_S44_L001_R1_001


title: ID150

description: GC.RM.9222.BT5011.150.F.215458_S46_L001_R1_001


title: Vero_NSP12 rep2 IP


title: ID149

description: GC.RM.9222.BT5011.149.F.215433_S45_L001_R1_001


title: ID151

description: GC.RM.9222.BT5011.151.F.215473_S47_L001_R1_001


title: ID144

description: GC.RM.9222.BT5011.144.F.215327_S40_L001_R1_001


title: UTHT1_ROW02_4


title: UTHT1_ROW02_8


title: ID146

description: GC.RM.9222.BT5011.146.F.215366_S42_L001_R1_001


title: UTHT1_ROW02_12


title: UTHT1_ROW02_11


title: UTHT1_ROW01_4


title: ID147

description: GC.RM.9222.BT5011.147.F.215391_S43_L001_R1_001


title: UTHT1_ROW02_14


title: ID142

description: GC.RM.9222.BT5011.142.F.215278_S38_L001_R1_001


title: UTHT1_ROW01_2


title: UTHT1_ROW02_9


title: UTHT1_ROW01_7


title: ID143

description: GC.RM.9222.BT5011.143.F.215300_S39_L001_R1_001


title: UTHT1_ROW01_15

description:
singlecell_countmatrix.tsv.gz
singlecell_metadata.tsv


title: ID145

description: GC.RM.9222.BT5011.145.F.215346_S41_L001_R1_001


title: UTHT1_ROW02_1


title: ID112

description: GC.RM.9222.BT5011.112.F.215496_S36_L001_R1_001


title: UTHT1_ROW01_16


title: ID109

description: GC.RM.9222.BT5011.109.F.215431_S33_L001_R1_001


title: ID111

description: GC.RM.9222.BT5011.111.F.215464_S35_L001_R1_001


title: ID108

description: GC.RM.9222.BT5011.108.F.215403_S32_L001_R1_001


title: UTHT5_ROW17_5


title: UTHT1_ROW01_10


title: UTHT5_ROW14_5


title: UTHT5_ROW26_4


title: ID107

description: GC.RM.9222.BT5011.107.F.215378_S31_L001_R1_001


title: ID106

description: GC.RM.9222.BT5011.106.F.215364_S30_L001_R1_001


title: UTHT5_ROW35_7


title: UTHT5_ROW15_6


title: UTHT5_ROW34_3


title: ID141

description: GC.RM.9222.BT5011.141.F.215261_S37_L001_R1_001


title: ID104

description: GC.RM.9222.BT5011.104.F.215319_S28_L001_R1_001


title: UTHT1_ROW01_17


title: ID103

description: GC.RM.9222.BT5011.103.F.215298_S27_L001_R1_001


title: UTHT5_ROW32_15


title: UTHT5_ROW09_7


title: ID110

description: GC.RM.9222.BT5011.110.F.215448_S34_L001_R1_001


title: ID102

description: GC.RM.9222.BT5011.102.F.215276_S26_L001_R1_001


title: ID052

description: GC.RM.9222.BT5011.52.F.215486_S24_L001_R1_001


title: UTHT5_ROW25_5


title: UTHT5_ROW40_3


title: UTHT5_ROW26_9


title: ID051

description: GC.RM.9222.BT5011.51.F.215461_S23_L001_R1_001


title: UTHT5_ROW24_7


title: ID049

description: GC.RM.9222.BT5011.49.F.215419_S21_L001_R1_001


title: ID050

description: GC.RM.9222.BT5011.50.F.215445_S22_L001_R1_001


title: ID048

description: GC.RM.9222.BT5011.48.F.215394_S20_L001_R1_001


title: ID105

description: GC.RM.9222.BT5011.105.F.215344_S29_L001_R1_001


title: ID046

description: GC.RM.9222.BT5011.46.F.215361_S18_L001_R1_001


title: UTHT5_ROW05_7

description:
singlecell_countmatrix.tsv.gz
singlecell_metadata.tsv


title: UTHT5_ROW28_1


title: UTHT5_ROW28_7


title: UTHT5_ROW30_7


title: ID045

description: GC.RM.9222.BT5011.45.F.215330_S17_L001_R1_001


title: ID044

description: GC.RM.9222.BT5011.44.F.215316_S16_L001_R1_001


title: UTHT5_ROW11_6


title: ID043

description: GC.RM.9222.BT5011.43.F215288_S15_L001_R1_001


title: ID041

description: GC.RM.9222.BT5011.41.F.215256_S13_L001_R1_001


title: ID101

description: GC.RM.9222.BT5011.101.F.215259_S25_L001_R1_001


title: UTHT5_ROW37_8


title: UTHT5_ROW38_1


title: ID042

description: GC.RM.9222.BT5011.42.F.215273_S14_L001_R1_001


title: UTHT5_ROW18_7


title: ID011

description: GC.RM.9222.BT5011.11.F.215459_S11_L001_R1_001

value: CON


title: UTHT5_ROW25_17


title: ID012

description: GC.RM.9222.BT5011.12F.215474_S12_L001_R1_001


title: UTHT5_ROW32_7


title: ID010

description: GC.RM.9222.BT5011.10.F.215434_S10_L001_R1_001


title: UTHT5_ROW19_3


title: UTHT5_ROW17_1


title: UTHT5_ROW03_18


title: ID007

description: GC.RM.9222.BT5011.7.F.215373_S7_L001_R1_001


title: UTHT5_ROW24_8


title: ID008

description: GC.RM.9222.BT5011.8.F.215392_S8_L001_R1_001


title: ID047

description: GC.RM.9222.BT5011.47.F.215375_S19_L001_R1_001


title: ID006

description: GC.RM.9222.BT5011.6.F.215347_S6_L001_R1_001


title: UTHT5_ROW21_1


title: ID009

description: GC.RM.9222.BT5011.9.F.215417_S9_L001_R1_001


title: ID005

description: GC.RM.9222.BT5011.5.F.215328_S5_L001_R1_001


title: ID004

description: GC.RM.9222.BT5011.4.F.215301_S4_L001_R1_001


title: UTHT5_ROW35_4

description:
singlecell_countmatrix.tsv.gz
singlecell_metadata.tsv


title: UTHT5_ROW16_13


title: UTHT5_ROW39_3


title: ID003

description: GC.RM.9222.BT5011.3.F.215286_S2_L001_R1_001


title: UTHT5_ROW38_18


title: UTHT5_ROW30_2


title: UTHT5_ROW37_1


title: B73_Node3

city: Qingdao

first: Fengxia

address: Number 72, Binhai Road

country: China

institute: Shandong University School of Life Science

data_processing:
The RNA was purified by electrophoresis through a TBE-urea polyacrylamide gel. The gel regions harboring 18-30 nt fragments were excised and the RNA recovered. The resulting population of sRNAs was 5' and 3' RNA adapter-ligated using T4 RNA ligase, and amplified for 18 PCR cycles
The amplicons were purified and sequenced using an Illumina/Solexa Genome Analyzer (Beijing Genomics Institute, Shenzhen, China).
Raw reads were trimmed by removing low-quality and adaptor sequences, then aligned to the A. thaliana genome using SOAP2 software.
Transcript frequency was calculated using the reads per kilobase per million reads method. Differentially transcribed genes were identified using a method modified from Audic and Claverie (1997). Significance was based on the P value and the false discovery rate (FDR) (Audic and Claverie, 1997).

organism: Zea mays

source_name: nodes

growth_protocol: The seedlings grew in the field for 28 days after germination, the three nodes together with internodes of the seedlings were extracted for RNA sequencing.

extract_protocol:
Total RNA was isolated using a RNeasy Mini Kit (Qiagen).
First strand cDNA was generated using reverse transcriptase and random primers. The constructed cDNA libraries was qualified and quantified with Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System, and then sequenced via Illumina HiSeqTM 2000 or other sequencer when necessary at the Beijing Genomics Institute, Shenzhen, China.

value: seedlings

tag: seedling age

value: nodes

tag: genotype

value: wild type


title: B73_Node1


title: ID002

description: GC.RM.9222.BT5011.2.F.215271_S1_L001_R1_001


title: B73_Node2


title: UTHT5_ROW19_4


title: UTHT5_ROW28_9


title: UTHT5_ROW10_9


title: UTHT5_ROW30_1


title: UTHT5_ROW10_2


title: ID001

description: GC.RM.9222.BT5011.1.F.215254_S3_L001_R1_001


title: UTHT5_ROW24_19


title: zmte1_Node3

value: zmet1 mutant


title: zmte1_Node2


title: UTHT5_ROW08_6


title: NHBE + SARS-CoV2 + HC [NHBE_37]

type: RNA

city: Munich

first: Ulrich

middle: M

last: Zissler

address: Biedersteiner Str. 29

department: Center of Allergy & Environment (ZAUM)

country: Germany

institute: Technical University of Munich & Helmholtz Center Munich

description:
NHBE_37
NHBE + SARS-CoV2 + HC

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green and 20 bit Tiff).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Agilent.SingleColor.28004 microarray, Software GeneSpring 14.5; Threshold: 1.0, Logbase: 2; Normalization: Quantile; Baseline Transformation: None; Filtered on Expression (20.0-100.0); Filtered on Flags (Detected, Not Detected); T test unpaired , P<=:0.05, FC>=1.5.

source_name: NHBE

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 17 ng RNA using the One-Color Agilent Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Hilden, GER). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: NHBEs were directly transferred into RNAcell protect reagent (Qiagen) and stored at -80°C until RNA extraction. Total RNA was extracted using RNeasy Mini Kit (Cat.-No. 74104, Qiagen, Hilden, Germany) with on-column DNase digestion (Cat.-No. 79254, DNase-Free DNase Set, Qiagen) for avoiding DNA contaminations (Zissler UM, 2016 Mucosal Immunology). RNA quantification was performed by ultraviolet–visible spectrophotometry (Nanodrop Technologies, Wilmington, DE, USA), for assessment of the RNA integrity by the RNA 6000 Nano Chip Kit with the Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

tag: cell type

value: Primary normal bronchial epithelial cells

tag: virus-stimulation

tag: treatment

value: Hydrocortisone

tag: donor no.


title: UTHT5_ROW16_5

value: cortex


title: zmte1_Node1


title: UTHT5_ROW29_2


title: UTHT5_ROW39_13


title: UTHT5_ROW24_3


title: UTHT5_ROW38_2


title: NHBE + SARS-CoV2 + HC [NHBE_33]

description:
NHBE_33
NHBE + SARS-CoV2 + HC


title: UTHT5_ROW06_7


title: UTHT5_ROW07_9


title: NHBE + SARS-CoV2 + HC [NHBE_32]

description:
NHBE_32
NHBE + SARS-CoV2 + HC


title: NHBE + SARS-CoV2 + HC [NHBE_36]

description:
NHBE_36
NHBE + SARS-CoV2 + HC


title: UTHT5_ROW37_19


title: UTHT5_ROW27_17


title: NHBE + SARS-CoV2 + Icatibant [NHBE_31]

description:
NHBE_31
NHBE + SARS-CoV2 + Icatibant

value: Icatibant


title: UTHT5_ROW38_7


title: NHBE + SARS-CoV2 + Icatibant [NHBE_28]

description:
NHBE_28
NHBE + SARS-CoV2 + Icatibant


title: UTHT5_ROW33_16


title: NHBE + SARS-CoV2 + HC [NHBE_34]

description:
NHBE_34
NHBE + SARS-CoV2 + HC


title: NHBE + SARS-CoV2 + HC [NHBE_35]

description:
NHBE_35
NHBE + SARS-CoV2 + HC


title: UTHT5_ROW40_18


title: NHBE + HC [NHBE_25]

description:
NHBE_25
NHBE + HC

value: no


title: NHBE + SARS-CoV2 + Icatibant [NHBE_30]

description:
NHBE_30
NHBE + SARS-CoV2 + Icatibant


title: UTHT5_ROW01_9


title: UTHT5_ROW09_9


title: NHBE + SARS-CoV2 + Icatibant [NHBE_29]

description:
NHBE_29
NHBE + SARS-CoV2 + Icatibant


title: UTHT5_ROW02_14


title: NHBE + HC [NHBE_22]

description:
NHBE_22
NHBE + HC


title: NHBE + SARS-CoV2 + Icatibant [NHBE_27]

description:
NHBE_27
NHBE + SARS-CoV2 + Icatibant


title: NHBE + HC [NHBE_21]

description:
NHBE_21
NHBE + HC


title: UTHT5_ROW11_2


title: NHBE + SARS-CoV2 + Icatibant [NHBE_26]

description:
NHBE_26
NHBE + SARS-CoV2 + Icatibant


title: NHBE + HC [NHBE_20]

description:
NHBE_20
NHBE + HC


title: NHBE + HC [NHBE_24]

description:
NHBE_24
NHBE + HC


title: NHBE + Icatibant [NHBE_18]

description:
NHBE_18
NHBE + Icatibant


title: NHBE + Icatibant [NHBE_17]

description:
NHBE_17
NHBE + Icatibant


title: UTHT5_ROW05_3


title: UTHT5_ROW34_5


title: UTHT5_ROW38_5


title: UTHT5_ROW38_12


title: NHBE + HC [NHBE_23]

description:
NHBE_23
NHBE + HC


title: NHBE + Icatibant [NHBE_15]

description:
NHBE_15
NHBE + Icatibant


title: UTHT5_ROW26_3


title: UTHT5_ROW15_20


title: UTHT5_ROW02_8


title: UTHT5_ROW33_18


title: UTHT5_ROW34_16


title: UTHT5_ROW10_15


title: UTHT5_ROW27_20


title: NHBE + SARS-CoV2 [NHBE_09]

description:
NHBE_09
NHBE + SARS-CoV2


title: NHBE + Icatibant [NHBE_19]

description:
NHBE_19
NHBE + Icatibant


title: NHBE Medium [NHBE_06]

description:
NHBE_06
NHBE Medium


title: NHBE + Icatibant [NHBE_14]

description:
NHBE_14
NHBE + Icatibant


title: NHBE Medium [NHBE_07]

description:
NHBE_07
NHBE Medium


title: NHBE Medium [NHBE_05]

description:
NHBE_05
NHBE Medium


title: NHBE + SARS-CoV2 [NHBE_12]

description:
NHBE_12
NHBE + SARS-CoV2


title: NHBE + SARS-CoV2 [NHBE_11]

description:
NHBE_11
NHBE + SARS-CoV2


title: UTHT5_ROW39_7


title: UTHT5_ROW06_3


title: UTHT5_ROW29_15


title: UTHT5_ROW15_8


title: UTHT5_ROW30_18


title: NHBE + SARS-CoV2 [NHBE_10]

description:
NHBE_10
NHBE + SARS-CoV2


title: UTHT5_ROW31_9


title: NHBE Medium [NHBE_02]

description:
NHBE_02
NHBE Medium


title: UTHT5_ROW06_8


title: UTHT5_ROW31_7


title: NHBE + Icatibant [NHBE_16]

description:
NHBE_16
NHBE + Icatibant


title: NHBE + SARS-CoV2 [NHBE_08]

description:
NHBE_08
NHBE + SARS-CoV2


title: NHBE + SARS-CoV2 [NHBE_13]

description:
NHBE_13
NHBE + SARS-CoV2


title: UTHT5_ROW29_7


title: UTHT5_ROW18_13


title: UTHT5_ROW20_18


title: UTHT5_ROW34_15


title: NHBE Medium [NHBE_03]

description:
NHBE_03
NHBE Medium


title: NHBE Medium [NHBE_04]

description:
NHBE_04
NHBE Medium


title: HZSYYY9

city: Hangzhou

first: Kai-ning

last: Lu

state: Zhejiang

address: No.238 Huansha Road, Shangcheng District

institute: Hangzhou First People's Hospital

description:
268
lncRNAs in papillary thyroid carcinoma (PTC) patients without Hashimoto's thyroiditis (HT).

hyb_protocol: Then, 1 μg of each labeled cRNA was fragmented by adding 5 μl of 10X Blocking Agent and 1 μl of 25X Fragmentation Buffer. The mixture was then heated to 60°C for 30 min. Finally, 25 μl of 2X GE Hybridization buffer was added to dilute the labeled cRNA, and 50 μl of hybridization solution was dispensed into the gasket slide and placed on the lncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent hybridization oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using an Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5 software package (Agilent Technologies). Low intensity lncRNAs were filtered (lncRNAs that at least 5 out of 10 samples have flags in Present or Marginal were chosen for further analysis).

source_name: Thyroid, papillary thyroid carcinoma (PTC) patients without Hashimoto's thyroiditis (HT)

label_protocol: The labeled cRNAs were purified using an RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured using a NanoDrop ND-1000 system.

extract_protocol:
Tissue samples were placed in a mortar, and the tissues were rapidly abraded with liquid nitrogen. Total RNA was extracted from 105 tissue samples using RNAiso Plus (TaKaRa, Code: D9108A, Japan) according to the manufacturer’s protocol.
RNA purity was evaluated using a NanoDrop ND-2000 (Thermo, USA) spectrophotometer based on the OD260 to OD280 ratio. RNA integrity was assessed using standard denaturing agarose gel electrophoresis.

tag: hashimoto's thyroiditis

value: papillary thyroid carcinoma

tag: gender

value: male


title: UTHT5_ROW11_7


title: HZSYYY8

description:
206
lncRNAs in papillary thyroid carcinoma (PTC) patients without Hashimoto's thyroiditis (HT).

value: female


title: UTHT5_ROW24_11


title: NHBE Medium [NHBE_01]

description:
NHBE_01
NHBE Medium


title: UTHT5_ROW24_16


title: K326Wz/Wz Wz-Wz rep2

city: Raleigh

first: Howard

middle: David

last: Shew

state: NC

address: 112 Derieux Pl

department: Entomology and Plant Pathology

institute: North Carolina State University

description:
WZ3-WZ-2
WZ3-WZ-2_S11

data_processing:
Sequence quality was assessed using FastQC v0.11.8.
Reads of all samples were aligned to the P. nicotianae genome (phytophthora_parasitica_inra_310.3.scaffolds.fasta) using Hisat2 v2.1.0.
Reads mapped to coding sequences of annotated genes were counted using featureCounts.
Reads of all samples were aligned to the Nicotiana tabacum genome using Hisat2 v2.1.0.
Reads mapped to coding sequences of annotated genes were counted using featureCounts.
Genome_build: phytophthora_parasitica_inra_310.3.scaffolds.fasta (https://www.ncbi.nlm.nih.gov/genome/11752?genome_assembly_id=49439)
Genome_build: Nitab4.5 ID (solgenomics)
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample.

organism:
Nicotiana tabacum
Phytophthora nicotianae

source_name: P. nicotianae infected tobacco roots

extract_protocol:
RNA was extracted from tobacco roots infected with P. nicotianae using Qiagen Plant RNeasy Kits.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: P. nicotianae infected tobacco roots

tag: tobacco genotype

tag: p. nicotianae isolate

value: Wz-Wz


title: HZSYYY6

description:
167
lncRNAs in papillary thyroid carcinoma (PTC) patients without Hashimoto's thyroiditis (HT).

tag: tissue


title: UTHT5_ROW08_14


title: HZSYYY10

description:
306
lncRNAs in papillary thyroid carcinoma (PTC) patients without Hashimoto's thyroiditis (HT).


title: HZSYYY1

description:
135
lncRNAs in papillary thyroid carcinoma (PTC) patients with Hashimoto's thyroiditis (HT).

source_name: Thyroid, papillary thyroid carcinoma (PTC) patients with Hashimoto's thyroiditis (HT)

value: yes


title: UTHT5_ROW29_16


title: K326Wz/Wz Wz-Wz rep1

description:
WZ3-WZ-1
WZ3-WZ-1_S10


title: UTHT5_ROW25_7


title: UTHT5_ROW11_20


title: glamblia_quantseq_rep2

city: Aurora

first: Olivia

last: Rissland

state: CO

address: 12801 East 17th Ave

department: BMG

institute: University of Colorado Denver

data_processing:
3'-end Seq libraries were sequenced at the Genomics and Microarray Shared Resource at the University of Colorado Denver Cancer Center on an Illumina MiSeq (MSQ-M01247R). Basecalling was completed with RTA version 1.18.54.0 and demultiplexing was done with bcl2fastq version 1.8.4
Adaptors were trimmed from 3'-end reads using Cutadapt v2.3. Libraries were aligned to the G. lamblia genome release 50 (2020-12-15) using STAR 2.5.2a (Dobin et al., 2013)
Downstream analyses were then performed with Python version 3.7.4, using in-house scripts.
Genome_build: G. lamblia release-50 https://giardiadb.org/giardiadb/app/downloads/release-50/GintestinalisAssemblageAWB/
Supplementary_files_format_and_content: BED file containing the coordinates of predicted cleavage sites based on assignment to the nearest open reading frame
Direct RNA Seq libraries were sequenced on a FLO-MIN106 flow-cell with a minION (MIN-101B) device in the Rissland lab at the University of Colorado Anschutz campus. Basecalling was completed by Guppy on the minKNOW software (Oxford Nanopore Technologies)
Reads were mapped by minimap2 (Li, 2018) to the G. lamblia genome release 50 (2020-12-15) obtained from GiardiaDB.org
Poly(A) tails were measured with the nanopolish software version 0.11.1 (Loman et al., 2015)
Mapped nanopore reads were assigned to their corresponding gene using featureCounts version 2.0.0 (Liao et al., 2014)
Genome_build: G. lamblia release-50 https://giardiadb.org/giardiadb/app/downloads/release-50/GintestinalisAssemblageAWB/
Supplementary_files_format_and_content: Tab separated values files containing poly(A) tail lengths for all reads

organism: Giardia duodenalis

source_name: Trophozoite

growth_protocol: G. lamblia trophozoites were grown in filtered modified TYI-S-33 medium in 10ml polystyrene tubes at 37°C

extract_protocol:
Poly(A) RNA was used to generate libraries with QuantSeq's 3' mRNA-Seq Library Prep Kit (REV) according to manufacturer's protocol and sequenced at the Genomics and Microarray Shared Resource at the University of Colorado Denver Cancer Center
RNA was extracted from trophozoites with hot acid phenol as described in Collart & Oliviero, Current protocols in molecular biology (1993)
See SAMPLES section

treatment_protocol: Cells were untreated

tag: developmental stage

value: Trophozoite


title: UTHT5_ROW21_16


title: Hicks Wz-Wz rep1

description:
WZ3-H-1
WZ3-H-1_S7

value: Hicks

value: Wz-H


title: HZSYYY4

description:
252
lncRNAs in papillary thyroid carcinoma (PTC) patients with Hashimoto's thyroiditis (HT).


title: UTHT5_ROW32_14


title: UTHT5_ROW19_16


title: K326Wz/Wz Wz-H rep2

description:
H3-WZ-2
H3-WZ-2_S5


title: K326Wz/Wz Wz-H rep1

description:
H3-WZ-1
H3-WZ-1_S4


title: UTHT5_ROW04_3


title: UTHT5_ROW07_20


title: UTHT5_ROW21_12


title: HZSYYY5

description:
269
lncRNAs in papillary thyroid carcinoma (PTC) patients with Hashimoto's thyroiditis (HT).


title: Hicks Wz-H rep1

description:
H3-H-3
H3-H-3_S1


title: HZSYYY2

description:
223
lncRNAs in papillary thyroid carcinoma (PTC) patients with Hashimoto's thyroiditis (HT).


title: Hicks Wz-H rep2

description:
H3-H-5
H3-H-5_S2


title: HZSYYY3

description:
237
lncRNAs in papillary thyroid carcinoma (PTC) patients with Hashimoto's thyroiditis (HT).


title: UTHT5_ROW12_5


title: HZSYYY7

description:
186
lncRNAs in papillary thyroid carcinoma (PTC) patients without Hashimoto's thyroiditis (HT).


title: UTHT5_ROW19_20


title: K326Wz/Wz Wz-Wz rep3

description:
WZ3-WZ-3
WZ3-WZ-3_S12


title: glamblia_quantseq_rep1


title: UTHT5_ROW01_1


title: UTHT5_ROW11_4


title: UTHT5_ROW31_2


title: UTHT5_ROW10_20


title: Hicks Wz-Wz rep2

description:
WZ3-H-2
WZ3-H-2_S8


title: 14_day_rep_1

city: Nashville

first: Erin

middle: R

last: Green

address: 1161 21st Ave South

department: Pathology, Microbiology, and Immunology

institute: Vanderbilt University Medical Center

library_source: genomic

data_processing:
library strategy: Tn-seq
Reads were trimmed
Reads were filtered for quality
Reads were mapped to the ATCC A. baumannii 17978 accession NZ_CP012004.
Using TUCF genomics analysis pipelines, a “Dval” score was assigned to each gene in each library pool, representing the aggregate number of reads for all transposon insertions within a gene in a given library sample, divided by the total number of predicted reads for that gene based on its size and the total number of reads obtained for the library pool.
Output Dval scores were normalized to input Dval scores to calculate a fitness score for each gene in each respective condition.
Fitness scores were Log2-transformed and an average Log2 fitness score was calculated for each gene in each condition analyzed (2 and 14 days of desiccation).
A Z-score was calculated that represents the number of standard deviations from the mean for each respective gene
Genome_build: Acinetobacter baumannii ATCC 17978 NZ_CP012004
Supplementary_files_format_and_content: File is in .xlsx format. Contains raw sequencing reads as well as normalized abundance (Dval) values and fitness analysis

organism: Acinetobacter baumannii

source_name: bacterial cells, pelleted

growth_protocol: Transposon library aliquots were inoculated into 10 mL LB medium (three biological replicates per condition) and grown for 8 hours at 37°C with shaking at 180 rpm. Bacteria were then harvested, washed twice in PBS, and resuspended in PBS at a concentration of 3x1011 CFU/mL.

extract_protocol:
Genomic DNA (gDNA) was extracted from bacterial pellets using the Qiagen DNeasy Blood and Tissue kit according to manufacturer’s instructions.
gDNA was sheared by sonication using the Covaris LE220 instrument to generate 350 bp fragments. Sheared DNA was treated with terminal deoxytransferase to generate a 3’ poly C-tail sequence, and two rounds of nested PCR were employed to amplify transposon junction regions. These products were multiplexed using 8-bp indexing primers and sequenced on the Illumina Hi-Seq 2500 at Tufts University Core Facility.

treatment_protocol: A volume of 100 mL (containing 3x1010 CFU) per sample was spread sterilely across the surface of a 100 mm polystyrene petri dish. Petri dishes were incubated at ambient humidity and temperature. After 2 and 14 days of desiccation, bacteria were rehydrated in 1 mL of PBS. For 2-day samples, 5 ml of rehydrated bacteria were diluted into 10 mL of LB. For 14-day samples, 50 ml of rehydrated bacteria were diluted into 10 mL of LB. Cultures were grown for 4 hours at 37°C with shaking at 180 rpm to enrich for surviving transposon mutants. In parallel, input samples were prepared by inoculating transposon library aliquots into 10 mL LB medium and growing for 8 hours at 37°C with shaking at 180 rpm. Following outgrowth, bacterial cultures were pelleted and stored at -80°C.

value: WT

value: 14-day desiccation


title: K326Wz/Wz Wz-H rep3

description:
H3-WZ-5
H3-WZ-5_S6


title: UTHT5_ROW06_6


title: UTHT5_ROW19_19


title: P.Intermedia_ApeK1_Hiseq_plate_1

city: Tainan City

first: Shu-Yun

last: Chen

address: No. 1 University Road

country: Taiwan

institute: NCKU

data_processing:
Library strategy: GBS
Illumina sequence read processing, mapping, and SNP calling involved using the TASSEL-GBS pipeline (Bradbury et al., 2007)
Genome_build: Pha_eq_chr19.fa
Supplementary_files_format_and_content: tab-delimited text files include SNP for each Sample

organism: Phalaenopsis x intermedia

source_name: Phalaenopsis leaf

extract_protocol:
DNA extraction in volved using the Qiagen DNeasy 96 Plant kit
For the two-enzyme GBS approach, HinpI 1 and ApeK1 were paired with HaeIII for library preparation following a previous protocol (Elshire et al., 2011) with minor modifications. Single-end sequencing of multiplex GBS libraries involved using Mi-seq (for HinpI 1 library) and Illumina HiSeq2500 (for ApeK I library) platforms.

value: Leaf

tag: enzyme


title: UTHT5_ROW40_6


title: Hicks Wz-Wz rep3

description:
WZ3-H-6
WZ3-H-6_S9


title: 2_day_rep_3

value: 2-day desiccation


title: UTHT5_ROW29_14


title: Hicks Wz-H rep3

description:
H3-H-6
H3-H-6_S3


title: UTHT5_ROW36_6


title: P.Intermedia_ApeK1_Hiseq_plate_2


title: UTHT5_ROW15_15


title: 2_day_rep_2


title: 2_day_rep_1


title: 2_day_input

value: input for 2-day desiccation


title: UTHT5_ROW05_10

value: cortex


title: 14_day_rep_2


title: UTHT5_ROW23_14


title: UTHT5_ROW36_12


title: UTHT5_ROW28_19


title: 14_day_input

value: input for 14-day desiccation


title: UTHT5_ROW14_14


title: UTHT5_ROW38_9


title: 14_day_rep_3


title: Liver_SDY_rep_1

city: Bodø

first: Ioannis

last: Konstantinidis

state: Nordland

address: Universitetsalléen 11

department: Faculty of Biosciences and Aquaculture

country: Norway

institute: Nord University

data_processing:
Raw sequences were adapter-trimmed and quality checked using Trim galore v0.4.4 (Babraham Bioinformatics, UK) with the following trimming parameters: -phred33, -fastqc, and -q20.
Alignments were performed using the hisat2 v2.1.0 platform with default parameters and the latest S. aurata genome assembly (GCA_900880675.2; NCBI, Bethesda, USA)
Count-based matrices were created for each sample using featureCounts v1.5.3 and they were then combined in R
Differential expression analysis was performed using DESeq2 (Anders and Huber, 2010) and the final list of differentially expressed genes (DEGs) was filtered accordingly (adjusted p value < 0.05) and absolute log2 fold change (FC) of 1.0
Genome_build: GCA_900880675.2; NCBI
Supplementary_files_format_and_content: Count-based matrices using featureCounts v1.5.3 in txt format

organism: Sparus aurata

source_name: Liver

extract_protocol:
Total RNA from each tissue was extracted from five randomly chosen specimens using the TRIzol reagent (Invitrogen, San Diego, CA, USA) following the manufacturer’s instructions
RNA-Seq libraries were prepared using the NEBNext ultra II directional RNA library preparation kit with a poly(A) mRNA magnetic isolation module (NEB #E7490) in accordance with the manufacturer’s protocol (New England BioLabs Inc., Ipswich, United Kingdom)

treatment_protocol: SDY diet had a 30% includion of Brewer's spent dry yeast, replacing 10% fish meal and 31.4% plant protein compared to the control diet.

tag: diet

value: SDY

value: Liver


title: Liver_Control rep_5

value: Control


title: UTHT5_ROW04_20


title: UTHT5_ROW31_14


title: Liver_SDY_rep_2


title: UTHT5_ROW37_12


title: UTHT5_ROW36_15


title: UTHT5_ROW21_5


title: UTHT5_ROW22_18


title: UTHT5_ROW21_9


title: Intestine_SDY_rep_5

source_name: Intestine

value: Intestine


title: Liver_SDY_rep_4


title: Liver_SDY_rep_5


title: UTHT5_ROW23_18


title: UTHT5_ROW15_7


title: Liver_SDY_rep_3


title: UTHT5_ROW29_20


title: UTHT5_ROW18_18


title: UTHT5_ROW11_14


title: Liver_Control rep_1


title: Liver_Control rep_3


title: UTHT5_ROW22_15


title: Intestine_SDY_rep_2


title: UTHT5_ROW20_19


title: Liver_Control rep_2


title: Intestine_Control rep_4


title: Liver_Control rep_4


title: Intestine_SDY_rep_4


title: UTHT5_ROW39_18


title: UTHT5_ROW12_16


title: Intestine_Control rep_3


title: Intestine_SDY_rep_1


title: UTHT5_ROW08_3


title: Intestine_Control rep_2


title: UTHT5_ROW33_8


title: Intestine_Control rep_5


title: Head_Kidney_SDY_rep_5

value: Head Kidney


title: UTHT5_ROW09_14


title: Intestine_Control rep_1


title: Intestine_SDY_rep_3


title: UTHT5_ROW03_16


title: UTHT5_ROW17_9


title: UTHT5_ROW05_19


title: Head_Kidney_SDY_rep_2


title: Head_Kidney_SDY_rep_1


title: Head_Kidney_Control rep_4


title: Head_Kidney_Control rep_5


title: UTHT5_ROW26_12


title: UTHT5_ROW15_13


title: UTHT5_ROW14_12


title: Head_Kidney_Control rep_3


title: UTHT5_ROW12_12


title: Head_Kidney_Control rep_1


title: UTHT5_ROW34_17


title: UTHT5_ROW29_1


title: Head_Kidney_SDY_rep_3


title: UTHT5_ROW28_17


title: UTHT5_ROW28_20


title: Head_Kidney_Control rep_2


title: UTHT5_ROW16_12


title: UTHT5_ROW06_16


title: UTHT5_ROW10_16


title: UTHT5_ROW17_10


title: STP1002, PO/QD, 5 mg/kg treated mouse 3

city: Seoul

first: Dong Young

last: Kim

address: 75 Nowon-ro

country: South Korea

institute: KIRAMS

description: Total RNA was isolated in Colo325DM xenograft tumor tissue.

hyb_protocol: Reporter and capture probes were hybridized to target genes for 16 h at 65 °C

scan_protocol: The target-probe complexes were aligned onto the nCounter cartridge, and the transcripts were counted via detection of the fluorescent barcodes within the reporter probe.

data_processing: Raw expression data were analyzed using the NanoSTRING software nSolver v4.0.70 with the Advanced Analysis Module v2.0 (RRID:SCR_003382).

source_name: Colo320DM xenograft tumor tissue

label_protocol: RNA was analyzed using the nCounter Human Tumor Signaling 360 Panel (#XT-CSPS-H-T360-12; NanoSTRING Technologies), which includes 760 tumor-related genes and 20 housekeeping genes.

growth_protocol: Each mouse was randomly assigned to study groups when the tumor sizes reached approximately 90 mm3.

extract_protocol: Total RNA was extracted from tumor tissue using a MasterPureTM RNA kit (#MC85200; Lucigen) according to the manufacturer's instructions. Samples with RIN values > 7.0, were included for gene expression analysis.

treatment_protocol: Oral administration, once daily, for 28 days

tag: disease state

value: colorectal cancer

value: 5 mpk STP1002 (TNKSi)


title: STP1002, PO/QD, 10 mg/kg treated mouse 2

description: Total RNA was isolated in Colo327DM xenograft tumor tissue.

value: 10 mpk STP1002 (TNKSi)


title: UTHT5_ROW14_8


title: UTHT5_ROW30_10


title: Head_Kidney_SDY_rep_4


title: STP1002, PO/QD, 10 mg/kg treated mouse 1

description: Total RNA was isolated in Colo326DM xenograft tumor tissue.


title: DMSO treated mouse 3

description: Total RNA was isolated in Colo322DM xenograft tumor tissue.

value: Vehicle


title: UTHT5_ROW04_15

description:
singlecell_countmatrix.tsv.gz
singlecell_metadata.tsv


title: STP1002, PO/QD, 5 mg/kg treated mouse 1

description: Total RNA was isolated in Colo323DM xenograft tumor tissue.


title: UTHT5_ROW15_16


title: UTHT5_ROW30_16


title: STP1002, PO/QD, 5 mg/kg treated mouse 2

description: Total RNA was isolated in Colo324DM xenograft tumor tissue.


title: UTHT5_ROW16_18


title: DMSO treated mouse 2

description: Total RNA was isolated in Colo321DM xenograft tumor tissue.


title: UTHT5_ROW40_14


title: UTHT5_ROW12_20


title: STP1002, PO/QD, 10 mg/kg treated mouse 3

description: Total RNA was isolated in Colo328DM xenograft tumor tissue.


title: UTHT5_ROW31_16


title: UTHT5_ROW30_14


title: UTHT5_ROW06_20


title: UTHT5_ROW36_14


title: JPS036 10µm_2

city: Leicester

first: Shaun

middle: Michael

last: Cowley

address: Henry Welcome Building, Leicester LE1 7RH

department: Molecular and Cell Biology

institute: University of Leicester

data_processing:
Hisat2 v2.2.1 alignment to GRCh38
Samtools v1.9 for sorting, bam coversion and indexing
LiBiNorm v2.5 run in (-z) htseq compatible mode for counting reads
DESeq2 was used for downstream processing
Genome_build: GRCh38 downloaded from HISAT2
https://genome-idx.s3.amazonaws.com/hisat/grch38_tran.tar.gz
Supplementary_files_format_and_content: counts

source_name: HCT116 from ATCC® CCL-247™

growth_protocol: The human colorectal carcinoma cell line HCT116 was obtained from ATCC (ATCC; CCL-247™). Cells were maintained in Dulbecco's Modified Eagle Medium (DMEM) (Gibco; 41963039), supplemented with 50 µL/mL (10% (v/v) foetal bovine serum (FBS) (Sigma; F9665) and 1.1 U/mL (1.1% v/v) Penicillin-Streptomycin-Glutamine (Gibco; 10378016); collectively termed M10 media. As an adherent cell line, HCT116 cells were seeded at a density of ~2.2 x 106 on 10 cm tissue culture treated plates for cell maintenance.

extract_protocol:
RNA was extracted from snap frozen pellets using Direct-Zol RNA MiniPrep kit (Zymo research #R2052)
Library preparation and sequencing was performed by Novogene (mRNA library preparation (poly A enrichment))

treatment_protocol: HCT116 cells were seeded at a density of 4x105 cells on 6-well plates for 24 hours prior to JPS0 treatment. Dilutions of JPS0S targeting class I HDACS were made from 50mM stock solutions synthesised and prepared in house by Joshua Smalley. HCT116 cells were then treated with JPS0 concentrations stated and harvested 24 hours later.

tag: cell line

tag: tumour type

value: colorectal carcinoma

value: Adult

value: male

tag: agent

value: JPS036 10microm


title: JPS026 5µm_2

value: JPS026 5microm


title: JPS035 10µm_2

value: JPS035 10microm


title: IAP CRTL 5µm_2

value: IAP CTRL 5microm


title: JPS016 10µm_2

value: JPS016 10microm


title: JPS039 10µm_2

value: JPS039 10microm


title: JPS014 10µm_2

value: JPS014 10microm


title: JPS004 10µm_2

value: JPS004 10microm


title: JPS027 5µm_2

value: JPS027 5microm


title: UTHT5_ROW16_16

value: cortex


title: DMSO treated mouse 1

description: Total RNA was isolated in Colo320DM xenograft tumor tissue.

value: colorectal cancer


title: CI-994 10µm_2

value: CI-994 10microm


title: UTHT5_ROW02_7


title: WT_2


title: UTHT5_ROW14_7


title: UTHT5_ROW36_16


title: UTHT5_ROW15_4