name: E-MTAB-6367:Genome-wide screen Pool9 A375 t15 PhenDC3 r1

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: human

text: Pool 9

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


name: E-MTAB-6367:Genome-wide screen Pool9 A375 t15 PhenDC3 r2

status: PUBLIC

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text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Cancer Research UK - Cambridge Institute and Department of Chemistry University of Cambridge

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text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: human

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text: Protocols: Cell Lines: HT1080, A375 (ATCC) and Plat-A (Cell Biolabs Inc) cell lines were cultured in DMEM medium (Gibco, cat #41966029) supplemented with 10% (v/v) heat inactivated FBS (Gibco, cat #10500064). All cell lines were grown at 37 °C in a 5% CO2 humidified atmosphere and regularly checked to be mycoplasma-free by RNA-capture ELISA. Cell line genotypes were certified by STR profiling. Quantification of live cell numbers: Throughout, live cell numbers (e.g. for plating cells for the cell titre glo assays, the screens and Incucyte experiments) were determined using the Muse Cell Analyser, ‘Count & Viability’ assay according to manufacturer’s instructions. Cells were diluted either 1:10 or 1:20 in ‘Muse Count & Viability kit’ solution, to give a viable cell concentration of 1-2 x 106 cells/mL, with ‘Events to Acquire’ parameter set at 1000 events. Determination of G-quadruplex ligand concentration for shRNA screens: Throughout, PDS and PhenDC3 were used as 50 mM stocks, dissolved in DMSO. GI20 values were calculated by treating A375 and HT1080 cells with serial dilutions of PDS and PhenDC3 for 96 h and determining cell death via a Cell Titre Glo assay (Promega) according to manufacturer’s protocol. Each serial dilution was replicated 4 times for 2 cell-seeding densities (1000/1500 cells per well). For both densities, curves were plotted averaging the 4 replicates in GraphPad Prism using a Non-Linear regression model, “dose-response - inhibition” equation [log(inhibitor) vs. normalised response - variable slope] and GI20 values calculated. The GI20 concentrations used represent an average for three separate assays per cell line and yielded the following concentrations used for the screens - A375: 10 μM PhenDC3 and 1.5 μM PDS; HT1080: 1 μM PhenDC3 and 0.5 μM PDS. Composition of and recombinant DNA production from shRNA libraries: The genome-wide screen uses the Transomic LMN shRNA library against the human protein coding genome, consisting of 113,002 total shRNAs, split between 12 pools for ease-of-handling (approximately 10,000 shRNAs per pool) with an average number of 6 optimised hairpins per gene. The pilot screen uses one pool (8) of the Transomic LMN shRNA library used in the genome-wide screen. The G-quadruplex focussed screen consists of a custom shRNA pool (Transomic) with the same LMN vector (8,018 shRNAs); this includes 1247 genes (7,436 shRNAs) uncovered in the GW screen (751 sensitisers and 496 upregulated genes), 116 other ‘interesting’ genes from the literature (439 shRNAs) and shRNAs targeting 37 olfactory receptors as non-targeting controls (143 shRNAs). In this custom pool, unlike the commercially available genome-wide library, we capped the number of shRNAs at 7 per gene (SF1B). The backbone of both libraries contains NeoR and ZsGreen markers to allow monitoring of infected cell lines by Geneticin (Gibco) selection and fluorescence (MacsQuant) respectively. Both libraries were provided as glycerol stocks. The bacterial density of these was determined by calculating the colony forming units (CFU) of dilutions of the original stock after plating on agar (O/N, 37 0C, 100 μg/ml ampicillin). Then, glycerol stocks were thawed completely and sufficient volume was taken (based on CFU) to ensure a minimum of 1000-fold hairpin representation, and inoculated in gigaprep bacterial cultures (LB media + 100 μg/ml ampicillin). Plasmid DNA was isolated from these cultures using ZR Gigaprep kit D4057 (Zymo research) according to manufacturer’s protocol and DNA was quantified by Nanodrop Onec. shRNA stable cell line creation: For the genome-wide screen, each pool was treated independently, necessitating the creation of 12 different polymorphic cell lines each containing an average of 10,000 shRNAs, for both HT1080 and A375, per replica (3 replicas, 36 polymorphic cell lines). Virus was produced using the Platinum-A packaging cell line and calcium phosphate transfection. 24 h after plating Platimum-A cells, media was replaced with DMEM medium supplemented with 1 % PenStrep and 10% (v/v) heat inactivated FBS. Then plasmid DNA isolated from the bacterial gigapreps were co-transfected with pCMV-VSV-G plasmid according to manufacturer’s protocol. Cells were also transfected with Pasha/DGCR8 siRNA (Qiagen) to increase viral titre. Immediately before adding the DNA-Pasha-transfection mixture, chloroquine (lysosomal inhibitor) is added to the plates at a final concentration 2.5 uM. 48 h after transfection virus was harvested and filter sterilised (0.45-μM) and stored at 4 0C for a maximum of 7 d. Viral titre was determined by performing mock infections with the experimental cell line and quantifying fluorescent cells, via flow cytometry (MacsQuant) 48 h after infection. For both the genome-wide and focussed-screen, 3.6 x 106 target cells were infected at a viral volume predicted to cause 30 % infection (MOI 0.3) to minimise multiple shRNA integrations per cell. This provides approximately 10 x 106 shRNA expressing cells (1000-fold shRNA representation). The virus was diluted in serum free media plus polybrene (8 μg/mL). Infections were carried out in triplicate, and treated as independent replicates hereafter. 48 h after infection cells were selected in 800 μg/ml (HT1080) and 1000 μg/ml (A375) geneticin for 7-9 days, concentrations determined via 7 day geneticin toxicity curves. Cell culture process for genome-wide and focussed pool of shRNAs: Following complete selection, a reference timepoint was harvested (t0) and cells were split into 3 x 15 cm plates per replica: PDS, PhenDC3 and DMSO vehicle control, each containing 8-10 x 106 cells to maintain 1000-fold hairpin representation. Every 72 h, cells were trypsinised, counted to determine the number of population doublings, and 10 x 106 (A375 GW and focussed) or 8 x 106 (HT1080) cells per replica replated in fresh drug/DMSO and media. The volume of DMSO used in the ‘vehicle’ condition is equal to the volume for 10 uM PhenDC3. The remaining drug treatments were also supplemented with DMSO to match this volume and keep the DMSO concentration equal between treatment, cell lines and screens. Therefore at all times, sufficient cell numbers were used so that a minimum of 1000 or 800 cells per shRNA were maintained (A375 and HT1080 respectively). A final timepoint (t15) was harvested after 15 population doublings. For each pool of the genome-wide screen, 12 samples were generated (t0, DMSO t15, PDS t15, PhenDC3 t15; 3 replicas each). Therefore, 144 samples of 10 x 106 cells were generated to cover the entire screen. For the focussed screen, for each cell line, 12 samples were generated (t0, DMSO t15, PDS t15, PhenDC3 t15; 3 replicas each). All PCR and Sequencing oligos were ordered from Sigma. Cell pellets (10 x 106 cells) were resuspended in PBS and gDNA extracted using QIAmp DNA Blood Maxi Kit (Qiagen) according to the manufacturer’s spin protocol, eluted in a final volume of 1200 μl and quantified by Qubit DNA HS Assay Kit. shRNA inserts were PCR-amplified from all gDNA in each sample, in multiple 50 μl reactions each using 1.5 μg gDNA, using KOD Hot Start DNA Polymerase and the following reagents (Merck Millipore): 5 μl 10 x buffer, 5 μl 2 mM each dNTPs, 4 μl MgSO4 (25 mM), 1.5 μl polymerase, 4 μl DMSO. Forward and reverse primers flanking the loop and antisense sequence of the hairpin region (Sigma) were used at a final concentration of 300 nM. PCR was performed under the following conditions: 98 oC for 5 min, then for 25 cycles of 98 oC for 35 s, 58 oC 35 s, 72 oC for 35 s, followed by 72 oC for 5 min. 1.2 mL of pooled PCR reaction were cleaned-up using QIAquick PCR purification kit (Qiagen) according to manufacturer’s protocol. 2 μg of this purified PCR product were PCR amplified in a second PCR step, using forward and reverse primers flanking the antisense sequence of the hairpin and containing the P5 and P7 flowcell adapters respectively. The PCR was performed in 8 x 50 μL reactions each containing 500 ng template DNA. The reverse primer contains TruSeq adapter small RNA Indexes to allow multiplexing of the samples, a 6 nucleotide barcode, denoted ‘nnnnnn’ below. PCR reagents were used as for the first PCR, with the exception of the primers, which were used at a final concentration 1.5 μM. The second PCR was performed under the following conditions: 98 oC for 5 min, then for 25 cycles of 94 oC for 35 s, 52 oC 35 s, 72 oC for 35 s, followed by 72 oC for 5 min. 200 μl of pooled secondary PCR product was cleaned up as previously and the desired product (~340 bp) was extracted using BluePippin 2 % Internal Standard Marker Kit (DF marker 100-600 bp; Sage Science), according to Manufacturer’s protocol using a broad range elution (300-400 bp). Individual samples were quantified using KAPA library quantification kit, Illumina platforms, BioRad CFX96 Instrument, No Rox according to manufacturer’s protocols and diluted to 4 nM in RNAse free water. For the GW screen samples, 24 libraries (2 pools) and for the focussed screen samples, 30 libraries (both cell lines) were combined to create a pooled 4 nM stock, with each sample having a unique TruSeq adapter.

characteristic: description

text: Pool 9

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

characteristic: title


name: E-MTAB-6367:Genome-wide screen Pool9 A375 t15 PhenDC3 r3

characteristic: ENA-FIRST-PUBLIC

text: Cancer Research UK - Cambridge Institute and Department of Chemistry University of Cambridge

text: public

text: ArrayExpress

text: human

text: Pool 9

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


name: E-MTAB-6367:Genome-wide screen Pool9 A375 t0 r1

characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

text: human

text: Pool 9

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Genome-wide screen Pool9 A375 t0 r1


name: E-MTAB-6367:Genome-wide screen Pool9 A375 t0 r2

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: human

text: Pool 9

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Genome-wide screen Pool9 A375 t0 r2


name: E-MTAB-6367:Genome-wide screen Pool9 A375 t0 r3

characteristic: External Id

text: public

text: ArrayExpress

text: human

text: Pool 9

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Genome-wide screen Pool9 A375 t0 r3


E-MTAB-6355:Sample 1

text: University of Bergen

characteristic: INSDC center name

text: public

text: E-MTAB-6355:Sample 1

tag: Namespace:University of Bergen

text: 24 to 30

unit: hour

characteristic: age

text: ArrayExpress

text: zebrafish

text: Protocols: For detailed protocols refer to Gagnon et al., 2014, Methods section with details in Supplementary Protocols. Here we listed shortened version as we can't upload images. There may be a more up-to-date version of this protocol on this website - http://labs.mcb.harvard.edu/schier/index.htmlTarget site selection for the initial screenBriefly, target sites were selected in exons across the genome that matched the sequence GG-N19-GG, GA-N19-GG, or AG-N19-GG. These sites were checked for uniqueness in RefSeq protein coding regions using Bowtie and the initially defined specificity rules, which suggested an intolerance for mismatches in the 3′ twelve bases of the target site.Cas9 cloning and protein expressionFor in vivo expression of Cas9, the Cas9 open reading frame was amplified from hCas9 and cloned into the pCS2 vector to generate pCS2-Cas9. For in vitro expression of Cas9, the hCas9 open reading frame cloned into pET-28b to generate pET-28b-Cas9-His. Cas9 protein was expressed in E. coli Rosetta cells (Novagen) using the auto-induction method, growing for 12 hours at 37°C, followed by 24 hour expression at 18°C. Purification was performed using his-tag resin (G-Biosciences). Buffers were 20 mM Tris pH 8, 30 mM Imidazole, 500 mM NaCl for washes and 20 mM Tris pH 8, 500 mM Imidazole, 500 mM NaCl for elutions. Fractions were dialyzed into 20 mM Tris, 200 mM KCl, 10 mM MgCl2 and single-use aliquots were frozen in liquid nitrogen and stored at −80°C. Plasmids are available from Addgene at http://www.addgene.org/Alex_Schier/.sgRNA template generation and transcriptionTo generate templates for sgRNA transcription, gene-specific oligonucleotides containing the T7 (5′-TAATACGACTCACTATA-3′) or SP6 (5′- ATTTAGGTGACACTATA-3′) promoter sequence, the 20 base target site without the PAM, and a complementary region were annealed to a constant oligonucleotide encoding the reverse-complement of the tracrRNA tail (Supplementary Figure S1 and Table S1). The ssDNA overhangs were filled in with T4 DNA polymerase (NEB), and the resulting sgRNA template were purified using Qiaquick columns (Qiagen). sgRNAs were transcribed using Megascript kits (Ambion). All sgRNAs were then DNase treated and precipitated with ammonium actetate/ethanol. Cas9 mRNA was transcribed from linearized template DNA using mMachine SP6 kit (Ambion), DNase treated, and precipitated with lithium chloride. RNA concentration was quantified using Nanodrop spectrophotometer and diluted and aliquoted as a 500 ng/ul 20× stock (sgRNAs) or 600 ng/ul 2× stock (Cas9 mRNA). Fish husbandry and microinjectionFor the initial screen, zebrafish TLAB strain zygotes were collected and injected through the chorion with a mix of 25 pg sgRNA, 300 pg Cas9 mRNA, and phenol red dye in a single mix. Embryos were grown to 24-30hpf and genomic DNA extracted from pools of 8-10 embryos using the HotSHOT method. For comparison between Cas9 mRNA and protein, higher levels of sgRNA were co-injected (200-300 pg). Cas9/sgRNA complex was formed by incubating protein with sgRNA at room temperature for 5 minutes before injection. Determination of somatic mutagenesis ratesTo determine indel percentage using sequencing, a fusion PCR method was used to attach Illumina P5 sequencing adapters and barcodes to amplicons designed to surround the target site. Amplicons were quantified by visualization on agarose gel before being pooled at roughly equal molar ratios. Pools of amplicons were gel extracted and sequenced with MiSeq Personal Sequencer (Illumina), 150 bp paired-end sequencing.

text: embryo

characteristic: developmental stage

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characteristic: loci sets

text: Danio rerio

text: Danio rerio

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characteristic: organism part

text: Danio rerio

text: TLAB

characteristic: strain

text: Sample 1


E-MTAB-6355:Sample 10

text: University of Bergen

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text: E-MTAB-6355:Sample 10

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text: 24 to 30

text: ArrayExpress

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text: zebrafish

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text: Danio rerio

text: Danio rerio

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text: Danio rerio

text: TLAB

text: Sample 10


E-MTAB-6355:Sample 11

characteristic: ENA-FIRST-PUBLIC

text: University of Bergen

text: public

text: E-MTAB-6355:Sample 11

text: 24 to 30

text: ArrayExpress

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characteristic: description

text: embryo

text: targeted mutation

text: Danio rerio

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text: Danio rerio

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text: Danio rerio

text: TLAB

text: Sample 11

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E-MTAB-6355:Sample 12

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text: University of Bergen

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text: ArrayExpress

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text: Danio rerio

text: Danio rerio

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text: Danio rerio

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E-MTAB-6355:Sample 13

text: University of Bergen

text: public

text: E-MTAB-6355:Sample 13

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

characteristic: developmental stage

text: targeted mutation

characteristic: genetic modification

characteristic: loci sets

text: Danio rerio

text: Danio rerio

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text: Danio rerio

text: TLAB

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text: Sample 13


E-MTAB-6355:Sample 14

text: University of Bergen

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text: E-MTAB-6355:Sample 14

characteristic: Submitter Id

text: 24 to 30

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text: Danio rerio

text: Danio rerio

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text: Danio rerio

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E-MTAB-6355:Sample 16

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text: University of Bergen

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text: zebrafish

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text: embryo

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text: Danio rerio

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text: Danio rerio

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text: Danio rerio

text: TLAB

text: Sample 16


E-MTAB-6355:Sample 19

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text: University of Bergen

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text: zebrafish

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text: Danio rerio

text: Danio rerio

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text: Danio rerio

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E-MTAB-6355:Sample 2

text: University of Bergen

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text: E-MTAB-6355:Sample 2

text: 24 to 30

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text: ArrayExpress

text: zebrafish

text: embryo

characteristic: developmental stage

text: targeted mutation

characteristic: genetic modification

characteristic: loci sets

text: Danio rerio

text: Danio rerio

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characteristic: organism part

text: Danio rerio

text: TLAB

text: Sample 2


E-MTAB-6355:Sample 3

text: University of Bergen

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text: E-MTAB-6355:Sample 3

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text: Danio rerio

text: Danio rerio

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text: Danio rerio

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text: Sample 3


E-MTAB-6355:Sample 4

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text: University of Bergen

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text: 24 to 30

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text: embryo

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text: Danio rerio

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text: Danio rerio

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text: Sample 4


E-MTAB-6355:Sample 5

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text: Danio rerio

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text: Danio rerio

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text: Danio rerio

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E-MTAB-6355:Sample 6

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text: ArrayExpress

text: zebrafish

text: embryo

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characteristic: loci sets

text: Danio rerio

text: Danio rerio

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text: Danio rerio

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text: Sample 6

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E-MTAB-6355:Sample 7

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text: E-MTAB-6355:Sample 7

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text: Danio rerio

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text: Danio rerio

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E-MTAB-6355:Sample 8

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text: Danio rerio

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text: Danio rerio

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text: Sample 8


E-MTAB-6355:Sample 9

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text: Danio rerio

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text: Danio rerio

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text: Sample 9


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text: Mixed

characteristic: cell type

text: chicken

text: Gallus gallus

characteristic: organism

text: Gallus gallus

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E-MTAB-6356:Sample 1

text: University of Bergen

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text: ArrayExpress

text: zebrafish

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characteristic: loci sets

text: Danio rerio

text: Danio rerio

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text: Danio rerio

text: TLAB

text: Sample 1

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E-MTAB-6356:Sample 12

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text: University of Bergen

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text: E-MTAB-6356:Sample 12

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text: 24 to 30

text: ArrayExpress

characteristic: broker name

text: zebrafish

characteristic: common name

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text: Danio rerio

text: Danio rerio

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characteristic: organism part

text: Danio rerio

text: TLAB

text: Sample 12


E-MTAB-6356:Sample 19

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text: University of Bergen

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text: E-MTAB-6356:Sample 19

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text: zebrafish

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text: embryo

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text: Danio rerio

text: Danio rerio

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text: Danio rerio

text: TLAB

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text: Sample 19


E-MTAB-6356:Sample 2

text: University of Bergen

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characteristic: INSDC last update

text: public

text: E-MTAB-6356:Sample 2

text: 24 to 30

characteristic: age

text: ArrayExpress

text: zebrafish

text: embryo

characteristic: developmental stage

text: targeted mutation

text: Danio rerio

characteristic: organism

text: Danio rerio

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text: Danio rerio

text: TLAB

text: Sample 2


E-MTAB-6356:Sample 3

characteristic: ENA-FIRST-PUBLIC

text: University of Bergen

text: public

characteristic: INSDC status

text: E-MTAB-6356:Sample 3

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

text: targeted mutation

characteristic: genetic modification

characteristic: loci sets

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

text: Sample 3

characteristic: title


E-MTAB-6356:Sample 4

text: University of Bergen

text: public

characteristic: SRA accession

text: E-MTAB-6356:Sample 4

characteristic: Submitter Id

text: 24 to 30

text: ArrayExpress

characteristic: broker name

text: zebrafish

characteristic: common name

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: whole organism

characteristic: organism part

text: Danio rerio

text: TLAB

text: Sample 4


E-MTAB-6356:Sample 5

characteristic: ENA-CHECKLIST

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characteristic: External Id

text: University of Bergen

characteristic: INSDC center name

text: public

text: E-MTAB-6356:Sample 5

text: 24 to 30

text: ArrayExpress

text: zebrafish

characteristic: description

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

text: Sample 5


E-MTAB-6356:Sample 6

text: University of Bergen

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6356:Sample 6

text: 24 to 30

characteristic: age

text: ArrayExpress

text: zebrafish

text: embryo

characteristic: developmental stage

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

characteristic: strain

text: Sample 6


E-MTAB-6356:Sample 7

characteristic: ENA-FIRST-PUBLIC

text: University of Bergen

text: public

characteristic: INSDC status

text: E-MTAB-6356:Sample 7

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

text: targeted mutation

characteristic: genetic modification

characteristic: loci sets

text: Danio rerio

characteristic: organism

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

text: Sample 7


E-MTAB-6356:Sample 8

text: University of Bergen

text: public

characteristic: SRA accession

text: E-MTAB-6356:Sample 8

characteristic: Submitter Id

text: 24 to 30

text: ArrayExpress

characteristic: broker name

text: zebrafish

characteristic: common name

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

text: Sample 8

characteristic: title


E-MTAB-6357:Sample 1

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Bergen

characteristic: INSDC center name

text: public

text: E-MTAB-6357:Sample 1

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: whole organism

characteristic: organism part

text: Danio rerio

text: TLAB

text: Sample 1


E-MTAB-6357:Sample 10

text: University of Bergen

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6357:Sample 10

text: 24 to 30

characteristic: age

text: ArrayExpress

text: zebrafish

characteristic: description

text: embryo

characteristic: developmental stage

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

text: Sample 10


E-MTAB-6357:Sample 11

characteristic: ENA-FIRST-PUBLIC

text: University of Bergen

text: public

characteristic: INSDC status

text: E-MTAB-6357:Sample 11

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

text: targeted mutation

characteristic: genetic modification

characteristic: loci sets

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

characteristic: strain

text: Sample 11


E-MTAB-6357:Sample 12

text: University of Bergen

text: public

characteristic: SRA accession

text: E-MTAB-6357:Sample 12

characteristic: Submitter Id

text: 24 to 30

text: ArrayExpress

characteristic: broker name

text: zebrafish

characteristic: common name

text: embryo

text: targeted mutation

text: Danio rerio

characteristic: organism

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

text: Sample 12


E-MTAB-6357:Sample 13

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Bergen

characteristic: INSDC center name

text: public

text: E-MTAB-6357:Sample 13

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

text: Sample 13

characteristic: title


E-MTAB-6357:Sample 14

text: University of Bergen

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6357:Sample 14

text: 24 to 30

characteristic: age

text: ArrayExpress

text: zebrafish

characteristic: description

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: whole organism

characteristic: organism part

text: Danio rerio

text: TLAB

text: Sample 14


E-MTAB-6357:Sample 15

characteristic: ENA-FIRST-PUBLIC

text: University of Bergen

text: public

characteristic: INSDC status

text: E-MTAB-6357:Sample 15

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

characteristic: developmental stage

text: targeted mutation

characteristic: genetic modification

characteristic: loci sets

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

text: Sample 15


E-MTAB-6357:Sample 16

text: University of Bergen

text: public

characteristic: SRA accession

text: E-MTAB-6357:Sample 16

characteristic: Submitter Id

text: 24 to 30

text: ArrayExpress

characteristic: broker name

text: zebrafish

characteristic: common name

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

characteristic: strain

text: Sample 16


E-MTAB-6357:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Bergen

characteristic: INSDC center name

text: public

text: E-MTAB-6357:Sample 2

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

text: targeted mutation

text: Danio rerio

characteristic: organism

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

text: Sample 2


E-MTAB-6357:Sample 3

text: University of Bergen

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6357:Sample 3

text: 24 to 30

characteristic: age

text: ArrayExpress

text: zebrafish

characteristic: description

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

text: Sample 3

characteristic: title


E-MTAB-6357:Sample 4

characteristic: ENA-FIRST-PUBLIC

text: University of Bergen

text: public

characteristic: INSDC status

text: E-MTAB-6357:Sample 4

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

characteristic: developmental stage

text: targeted mutation

characteristic: genetic modification

text: Danio rerio

text: Danio rerio

text: whole organism

characteristic: organism part

text: Danio rerio

text: TLAB

text: Sample 4


E-MTAB-6357:Sample 5

text: University of Bergen

text: public

characteristic: SRA accession

text: E-MTAB-6357:Sample 5

characteristic: Submitter Id

text: 24 to 30

text: ArrayExpress

characteristic: broker name

text: zebrafish

characteristic: common name

text: embryo

text: targeted mutation

characteristic: loci sets

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

text: Sample 5


E-MTAB-6357:Sample 6

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Bergen

characteristic: INSDC center name

text: public

text: E-MTAB-6357:Sample 6

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

characteristic: strain

text: Sample 6


E-MTAB-6357:Sample 7

text: University of Bergen

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6357:Sample 7

text: 24 to 30

characteristic: age

text: ArrayExpress

text: zebrafish

characteristic: description

text: embryo

text: targeted mutation

text: Danio rerio

characteristic: organism

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

text: Sample 7


E-MTAB-6357:Sample 8

characteristic: ENA-FIRST-PUBLIC

text: University of Bergen

text: public

characteristic: INSDC status

text: E-MTAB-6357:Sample 8

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

characteristic: developmental stage

text: targeted mutation

characteristic: genetic modification

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

text: Sample 8

characteristic: title


E-MTAB-6357:Sample 9

text: University of Bergen

text: public

characteristic: SRA accession

text: E-MTAB-6357:Sample 9

characteristic: Submitter Id

text: 24 to 30

text: ArrayExpress

characteristic: broker name

text: zebrafish

characteristic: common name

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: whole organism

characteristic: organism part

text: Danio rerio

text: TLAB

text: Sample 9


E-MTAB-6358:Sample 1

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Bergen

characteristic: INSDC center name

text: public

text: E-MTAB-6358:Sample 1

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

text: targeted mutation

characteristic: loci sets

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

text: Sample 1


E-MTAB-6358:Sample 12

text: University of Bergen

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6358:Sample 12

text: 24 to 30

characteristic: age

text: ArrayExpress

text: zebrafish

characteristic: description

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

characteristic: strain

text: Sample 12


E-MTAB-6358:Sample 15

characteristic: ENA-FIRST-PUBLIC

text: University of Bergen

text: public

characteristic: INSDC status

text: E-MTAB-6358:Sample 15

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

characteristic: developmental stage

text: targeted mutation

characteristic: genetic modification

text: Danio rerio

characteristic: organism

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

text: Sample 15


E-MTAB-6358:Sample 19

text: University of Bergen

text: public

characteristic: SRA accession

text: E-MTAB-6358:Sample 19

characteristic: Submitter Id

text: 24 to 30

text: ArrayExpress

characteristic: broker name

text: zebrafish

characteristic: common name

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

text: Sample 19

characteristic: title


E-MTAB-6358:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Bergen

characteristic: INSDC center name

text: public

text: E-MTAB-6358:Sample 2

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: whole organism

characteristic: organism part

text: Danio rerio

text: TLAB

text: Sample 2


E-MTAB-6358:Sample 3

text: University of Bergen

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6358:Sample 3

text: 24 to 30

characteristic: age

text: ArrayExpress

text: zebrafish

characteristic: description

text: embryo

text: targeted mutation

characteristic: loci sets

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

text: Sample 3


E-MTAB-6358:Sample 4

characteristic: ENA-FIRST-PUBLIC

text: University of Bergen

text: public

characteristic: INSDC status

text: E-MTAB-6358:Sample 4

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

characteristic: developmental stage

text: targeted mutation

characteristic: genetic modification

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

characteristic: strain

text: Sample 4


E-MTAB-6358:Sample 5

text: University of Bergen

text: public

characteristic: SRA accession

text: E-MTAB-6358:Sample 5

characteristic: Submitter Id

text: 24 to 30

text: ArrayExpress

characteristic: broker name

text: zebrafish

characteristic: common name

text: embryo

text: targeted mutation

text: Danio rerio

characteristic: organism

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

text: Sample 5


E-MTAB-6358:Sample 6

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Bergen

characteristic: INSDC center name

text: public

text: E-MTAB-6358:Sample 6

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

text: Sample 6

characteristic: title


E-MTAB-6358:Sample 7

text: University of Bergen

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6358:Sample 7

text: 24 to 30

characteristic: age

text: ArrayExpress

text: zebrafish

characteristic: description

text: embryo

text: targeted mutation

text: Danio rerio

text: Danio rerio

text: whole organism

characteristic: organism part

text: Danio rerio

text: TLAB

text: Sample 7


E-MTAB-6358:Sample 8

characteristic: ENA-FIRST-PUBLIC

text: University of Bergen

text: public

characteristic: INSDC status

text: E-MTAB-6358:Sample 8

text: 24 to 30

text: ArrayExpress

text: zebrafish

text: embryo

characteristic: developmental stage

text: targeted mutation

characteristic: genetic modification

characteristic: loci sets

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: TLAB

text: Sample 8


E-MTAB-6348:Sample 1

text: The Francis Crick Institute

text: public

characteristic: SRA accession

text: E-MTAB-6348:Sample 1

tag: Namespace:The Francis Crick Institute

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: HM1 ESC

characteristic: cell line

text: mouse neural progenitor cell

characteristic: cell type

text: house mouse

characteristic: common name

text: Protocols: To obtain neural progenitors with anterior, hindbrain or spinal cord neural identity, ESCs were differentiated as previously described (https://doi.org/10.1371/journal.pbio.1001937 Gouti et al, 2014). Briefly, ESCs were dissociated with 0.05% trypsin, and plated on gelatin-coated plates for two sequential 20 minute periods in ESC medium to separate them from their feeders. To start the differentiation, cells remaining in the supernatant were pelleted by centrifugation, washed in PBS, and pelleted again. Cells were counted and resuspended in N2B27 medium containing 10ng/ml bFGF to a concentration of 106 cells per ml, and 50,000 cells per 35mm CELLBIND dish were plated. To generate anterior neural progenitors, the cells were grown up to day 3 in N2B27 + 10ng/ml bFGF, followed by N2B27 + 500nM smoothened agonist (SAG; Calbiochem) from day 3-5. To generate hindbrain neural progenitors, cells were cultured under the same conditions as the anterior, but were additionally exposed to 100nM retinoic acid (RA; Sigma) from day 3-5. To generate spinal cord neural progenitors, cells were cultured with N2B27 + 10ng/ml bFGF until day 2, N2B27 + 10ng/ml bFGF + 5 micro M CHIR99021 until day 3, and N2B27 + 100nM RA + 500nM SAG until day 5. For all differentiations, media changes were made every 24 hours from day 2. Samples were collected as previously described (Kutejova et al., 2016). 10-30 million cells from day 5 hindbrain or day 5 spinal cord neural progenitors were collected from plates using scrapers and crosslinked in 1% formaldehyde for 20 min at 4 degrees. Chromatin was sonicated using a Diagenode Bioruptor (using a cycle of 30sec on, 30 sec off) until fragments were between 200-400bp. Samples were decrosslinked and purified using the Qiagen MinElute kit following manufacturer’s instructions. Chromatin immunoprecipitation was performed as previously described in Kutejova et al., 2016. 3ug of Sox2 antibody (Santa cruz antibody SC-17320X) was incubated together with cell lysate overnight at 4°C on a rotating wheel. Immunoprecipitation of chromatin fragments were captured using Protein G-coupled Dynabeads (Life Technologies). Samples were decrosslinked and purified using the Qiagen MinElute kit as per manufacturer’s instructions. To generate libraries, approximately 10ng ChIP DNA and 10ng input DNA was used for each condition. Libraries were generated by by blunt-end repair, dA-tailing, and ligation of Illumina adaptors using the KAPA Hyper Prep Kit following manufacturer’s instructions. Libraries were size-selected to obtain fragments between 250-400bps using an E-Gel EX Agarose Gel. Library quality control was carried out using the Bioanalyzer High-Sensitivity DNA analysis kit as per manufacturer’s instructions.

text: embryo

text: normal

characteristic: disease

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: mouse embryonic stem cell

characteristic: progenitor cell type

text: hindbrain neural progenitor differentiation

characteristic: protocol

text: Mus musculus

characteristic: strain

text: Sample 1


E-MTAB-6348:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6348:Sample 2

text: ArrayExpress

text: HM1 ESC

text: mouse neural progenitor cell

text: house mouse

characteristic: description

text: embryo

text: normal

text: Mus musculus

characteristic: organism

text: Mus musculus

text: inner cell mass

text: mouse embryonic stem cell

text: Mus musculus

text: Sample 2

characteristic: title


E-MTAB-6348:Sample 3

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6348:Sample 3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: HM1 ESC

text: mouse neural progenitor cell

text: house mouse

text: embryo

characteristic: developmental stage

text: normal

text: Mus musculus

text: Mus musculus

text: inner cell mass

characteristic: organism part

text: mouse embryonic stem cell

text: Mus musculus

text: Sample 3


E-MTAB-6348:Sample 4

text: The Francis Crick Institute

text: public

text: E-MTAB-6348:Sample 4

text: ArrayExpress

text: HM1 ESC

characteristic: cell line

text: mouse neural progenitor cell

characteristic: cell type

text: house mouse

characteristic: common name

text: embryo

text: normal

characteristic: disease

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: mouse embryonic stem cell

characteristic: progenitor cell type

characteristic: protocol

text: Mus musculus

characteristic: strain

text: Sample 4


E-MTAB-6348:Sample 5

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6348:Sample 5

text: ArrayExpress

text: HM1 ESC

text: mouse neural progenitor cell

text: house mouse

characteristic: description

text: embryo

text: normal

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: mouse embryonic stem cell

text: spinal cord neural progenitor differentiation

text: Mus musculus

text: Sample 5


E-MTAB-6348:Sample 6

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6348:Sample 6

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: HM1 ESC

text: mouse neural progenitor cell

text: house mouse

text: embryo

text: normal

text: Mus musculus

characteristic: organism

text: Mus musculus

text: inner cell mass

text: mouse embryonic stem cell

text: Mus musculus

text: Sample 6

characteristic: title


E-MTAB-6348:Sample 7

text: The Francis Crick Institute

text: public

text: E-MTAB-6348:Sample 7

text: ArrayExpress

text: HM1 ESC

characteristic: cell line

text: mouse neural progenitor cell

characteristic: cell type

text: house mouse

characteristic: common name

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: Mus musculus

text: Mus musculus

text: inner cell mass

characteristic: organism part

text: mouse embryonic stem cell

characteristic: progenitor cell type

text: Mus musculus

text: Sample 7


E-MTAB-6348:Sample 8

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-6348:Sample 8

text: ArrayExpress

text: HM1 ESC

text: mouse neural progenitor cell

text: house mouse

text: embryo

text: normal

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: mouse embryonic stem cell

characteristic: protocol

text: Mus musculus

characteristic: strain

text: Sample 8


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi (SA), Italy

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fibroblast

text: human

text: Protocols: CAFs at 70-80% of confluence were treated with vehicle (-) or with GW4064 (6μM) for 8-12 hrs. Then, cells were washed twice and cultured with serum-free media for the following 24 hrs. Afterwards, conditioned medium was collected, centrifuged to remove cellular debris, and used in respective co-culture experiments. Total RNA was extracted from cells using RNeasy columns (Qiagen, Germantown, MD, USA) and gene expression was assessed by real-time RT-PCR. High quality RNA from three-independent purifications for each experimental point was used for library preparation. Indexed libraries were prepared from 1μg/ea. of purified RNA with TruSeq-RNA-Sample-Prep-Kit (Illumina) following suppliers.

characteristic: description

text: breast carcinoma

text: Homo sapiens

text: Homo sapiens

text: breast

text: tumour

characteristic: sampling site

text: Homo sapiens


text: Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi (SA), Italy

text: public

text: ArrayExpress

text: fibroblast

characteristic: cell type

text: human

characteristic: common name

text: breast carcinoma

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

characteristic: organism part

text: tumour

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:German Centre for Integrative Biodiversity Research (iDiv)

text: green lizard

text: Lacerta viridis

text: Lacerta viridis

text: Female

characteristic: sex

text: Heart

characteristic: tissue type

text: L. viridis transcriptome Illumina reads


characteristic: ENA-FIRST-PUBLIC

text: German Centre for Integrative Biodiversity Research (iDiv)

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: green lizard

text: Lacerta viridis

text: Lacerta viridis

text: Female

text: Brain

text: L. viridis Transcriptome Illumina reads


text: public

text: green lizard

characteristic: common name

text: Lacerta viridis

text: Lacerta viridis

text: Female

text: Ovary

text: L. viridis transcriptome Illumina reads


text: public

text: green lizard

text: Lacerta viridis

text: Lacerta viridis

text: Female

text: Liver

text: L. viridis transcriptome Illumina reads


text: Clostridium perfringens ATCC 13124

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: Clostridium perfringens ATCC 13124

text: Clostridium perfringens ATCC 13124

text: Clostridium perfringens ATCC 13124

characteristic: subject id


text: public

text: green lizard

text: Lacerta viridis

characteristic: organism

text: Lacerta viridis

text: Female

text: Kidney

text: L. viridis transcriptome Illumina reads


text: HARVARD MEDICAL SCHOOL

text: public

tag: Namespace:HARVARD MEDICAL SCHOOL

text: African forest elephant

text: Forest elephant genome from Central African Republic

characteristic: description

text: Loxodonta cyclotis

text: Loxodonta cyclotis

text: L. cyclotis_A

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: HARVARD MEDICAL SCHOOL

text: public

text: African savanna elephant

text: Savanna elephant genome from Kenya

text: Loxodonta africana

text: Loxodonta africana

text: L. africana_B


characteristic: External Id

text: HARVARD MEDICAL SCHOOL

characteristic: INSDC center name

text: public

text: African savanna elephant

text: Savanna elephant genome from South Africa

text: Loxodonta africana

text: Loxodonta africana

text: L. africana_C


text: HARVARD MEDICAL SCHOOL

characteristic: INSDC first public

text: public

text: Asiatic elephant

text: Asian elephant genome from Myanmar

text: Elephas maximus

text: Elephas maximus

text: E. maximus_D


text: HARVARD MEDICAL SCHOOL

text: public

text: Asiatic elephant

text: Asian elephant genome from Borneo

text: Elephas maximus

text: Elephas maximus

text: E. maximus_E


text: HARVARD MEDICAL SCHOOL

text: public

text: African forest elephant

text: Forest elephant genome from Sierra Leone

text: Loxodonta cyclotis

text: Loxodonta cyclotis

text: L. cyclotis_F


text: HARVARD MEDICAL SCHOOL

text: public

text: woolly mammoth

text: Woolly mammoth genome-wide data from Taimyr peninsula, Russia

text: Mammuthus primigenius

text: Mammuthus primigenius

text: M. primigenius_G


text: HARVARD MEDICAL SCHOOL

text: public

text: woolly mammoth

text: Woolly mammoth genome-wide data from Alaska, USA

text: Mammuthus primigenius

text: Mammuthus primigenius

text: M. primigenius_H


text: HARVARD MEDICAL SCHOOL

text: public

text: American mastodon

text: American mastodon genome from Alaska, USA

text: Mammut americanum

text: Mammut americanum

text: M. americanum_I


text: HARVARD MEDICAL SCHOOL

text: public

text: Straight-tusked elephant genome from Germany

text: Elephas antiquus

text: Elephas antiquus

text: P. antiquus_N


text: HARVARD MEDICAL SCHOOL

text: public

text: woolly mammoth

text: Woolly mammoth genome-wide data from Yamal peninsula, Russia

text: Mammuthus primigenius

text: Mammuthus primigenius

text: M. primigenius_S


text: HARVARD MEDICAL SCHOOL

text: public

text: Columbian mammoth

text: Columbian mammoth genome from Wyoming, USA

text: Mammuthus columbi

text: Mammuthus columbi

text: M. columbi_U


text: HARVARD MEDICAL SCHOOL

text: public

text: woolly mammoth

text: Woolly mammoth genome from Ywyoming, USA

text: Mammuthus primigenius

text: Mammuthus primigenius

text: M. primigenius_V


text: HARVARD MEDICAL SCHOOL

text: public

text: American mastodon

text: American mastodon genome-wide data from Gulf of Maine, USA

text: Mammut americanum

text: Mammut americanum

text: M. americanum_X


text: Shanghai Jiao Tong University

text: public

tag: Namespace:Shanghai Jiao Tong University

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: human

text: Protocols: Human liver cells and liver cancer cells were purchased from the Shanghai Cell Collection (Shanghai, China). All cells were cultured in Dulbecco’s modified Eagle’s medium with 10% feta calf serum (FCS), penicillin (50 U/ml), streptomycin (50 mg/ml), and glutamine (2mM) at 37°C in a 5% CO2 humidified atmosphere. Given the functional involvement of NUDT21 in APA formation and its tumor suppression activities mentioned above, we hypothesized that NUDT21 exert its tumor suppression, at least in part, by influencing APA and 3’UTR. To test this hypothesis, we aimed to examine all instances of NDUT21-related 3’UTR alteration in HCC cells. To this end, we generated NUDT21 overexpression line in Hep3B and NUDT21 knockout line in HL7702, and identified poly(A) sites with 3T-seq. RNA was isolated from using Trizol (Invitrogen), reverse-transcribed using RevertAid™ First Strand cDNA Synthesis Kit (Fermentas); Quantitative PCR was performed using gene-specific primer pairs and SYBR Green. 1µg total RNA was used to generate cDNA with Superscript II reverse transcriptase (Invitrogen) according to the manufacturer’s instructions using 3’RACE-RT as a primer. The ﬁrst PCR was done with a PSMB2 or CXXC5-speciﬁc forward primer and Outer as reverse primer. Nested PCR was done with a nested PSMB2 or CXXC5-speciﬁc forward primer and inner as reverse primer. The PCR product from the nested PCR was separated on an agarose gel, cloned and sequenced.

text: hepatocellular carcinoma

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: liver

characteristic: organism part

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: Shanghai Jiao Tong University

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: human

text: hepatocellular carcinoma

text: NUDT21 overexpression

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens


text: Shanghai Jiao Tong University

text: public

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: normal

text: wild type genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: liver

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Shanghai Jiao Tong University

text: public

text: ArrayExpress

text: human

text: normal

text: NUDT21 knockdown by shRNA

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens

characteristic: title


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Lacerta bilineata

text: Lacerta bilineata

text: Female

characteristic: sex

text: Heart

characteristic: tissue type

text: L. bilineata transcriptome Illumina data


text: public

text: Lacerta bilineata

text: Lacerta bilineata

text: Female

text: Brain


text: public

text: Lacerta bilineata

text: Lacerta bilineata

text: Female

text: Ovary


text: public

text: Lacerta bilineata

text: Lacerta bilineata

text: Female

text: Kidney


text: public

text: Lacerta bilineata

text: Lacerta bilineata

text: Female

text: Liver


text: ENS Lyon

text: public

tag: Namespace:ENS Lyon

text: Old Blush

characteristic: cultivar

text: Genome assembly of Rosa chinensis cv 'Old Blush' (heterozygous)

text: Old Blush

characteristic: genotype

text: Axenic in-vitro culture

characteristic: growth condition

text: from École normale supérieure, Lyon, France

characteristic: individual

text: Rosa chinensis

text: Leaves

characteristic: organism part

text: Diploid

characteristic: ploidy

text: Rosa chinensis

text: Rosa chinensis cv 'Old Blush' genome sequence


characteristic: ENA-FIRST-PUBLIC

text: DALHOUSIE UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:DALHOUSIE UNIVERSITY

characteristic: Submitter Id

text: First run of the V4-V5 HMP mock community.

text: metagenomes

text: metagenomes


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: DALHOUSIE UNIVERSITY

text: public

text: Raw Sequence Data for the mock communities sequenced by the Langille Lab.

characteristic: description

text: metagenomes

characteristic: organism

text: metagenomes

characteristic: title


characteristic: External Id

text: German Centre for Integrative Biodiversity Research (iDiv)

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: green lizard

characteristic: common name

text: Hungary

characteristic: geographic location (country and/or sea)

text: Tokaj

characteristic: geographic location (region and locality)

text: Lacerta viridis

text: Lacerta viridis

text: Female

characteristic: sex

text: L. viridis genome Illumina reads


rice GP104

characteristic: ENA-FIRST-PUBLIC

text: NCGR

text: public

text: rice GP104

text: rice

text: Oryza sativa

text: Oryza sativa


rice GP124

text: NCGR

characteristic: INSDC last update

text: public

text: rice GP124

text: rice

text: Oryza sativa

text: Oryza sativa


rice GP22

text: NCGR

text: public

characteristic: INSDC status

text: rice GP22

text: rice

text: Oryza sativa

text: Oryza sativa


rice GP3

text: NCGR

text: public

characteristic: SRA accession

text: rice GP3

text: rice

text: Oryza sativa

text: Oryza sativa


rice GP39

text: NCGR

text: public

text: rice GP39

characteristic: Submitter Id

text: rice

text: Oryza sativa

text: Oryza sativa


rice GP51

characteristic: ENA-CHECKLIST

text: NCGR

text: public

text: rice GP51

text: rice

text: Oryza sativa

text: Oryza sativa


rice GP536

characteristic: ENA-LAST-UPDATE

text: NCGR

text: public

text: rice GP536

text: rice

text: Oryza sativa

text: Oryza sativa


rice GP540

text: NCGR

text: public

text: rice GP540

text: rice

text: Oryza sativa

text: Oryza sativa


rice GP551

text: NCGR

text: public

text: rice GP551

text: rice

text: Oryza sativa

text: Oryza sativa


rice GP567

text: NCGR

text: public

text: rice GP567

text: rice

text: Oryza sativa

text: Oryza sativa


rice GP62

text: NCGR

text: public

text: rice GP62

text: rice

text: Oryza sativa

text: Oryza sativa


rice GP640

text: NCGR

text: public

text: rice GP640

text: rice

text: Oryza sativa

text: Oryza sativa


rice GP669

text: NCGR

text: public

text: rice GP669

text: rice

text: Oryza sativa

text: Oryza sativa


rice GP677

text: NCGR

text: public

text: rice GP677

text: rice

text: Oryza sativa

text: Oryza sativa


rice GP72

text: NCGR

text: public

text: rice GP72

text: rice

text: Oryza sativa

text: Oryza sativa


rice GP77

text: NCGR

text: public

text: rice GP77

text: rice

text: Oryza sativa

text: Oryza sativa


rice HP103

text: NCGR

text: public

text: rice HP103

text: rice

text: Oryza sativa

text: Oryza sativa


rice HP119

text: NCGR

text: public

text: rice HP119

text: rice

text: Oryza sativa

text: Oryza sativa


rice HP14

text: NCGR

text: public

text: rice HP14

text: rice

text: Oryza sativa

text: Oryza sativa


rice HP263

text: NCGR

text: public

text: rice HP263

text: rice

text: Oryza sativa

text: Oryza sativa


rice HP274

text: NCGR

text: public

text: rice HP274

text: rice

text: Oryza sativa

text: Oryza sativa


rice HP314

text: NCGR

text: public

text: rice HP314

text: rice

text: Oryza sativa

text: Oryza sativa


rice HP327

text: NCGR

text: public

text: rice HP327

text: rice

text: Oryza sativa

text: Oryza sativa


rice HP38

text: NCGR

text: public

text: rice HP38

text: rice

text: Oryza sativa

text: Oryza sativa


rice HP383

text: NCGR

text: public

text: rice HP383

text: rice

text: Oryza sativa

text: Oryza sativa


rice HP390

text: NCGR

text: public

text: rice HP390

text: rice

text: Oryza sativa

text: Oryza sativa


rice HP396

text: NCGR

text: public

text: rice HP396

text: rice

text: Oryza sativa

text: Oryza sativa


rice HP407

text: NCGR

text: public

text: rice HP407

text: rice

text: Oryza sativa

text: Oryza sativa


rice HP44

text: NCGR

text: public

text: rice HP44

text: rice

text: Oryza sativa

text: Oryza sativa


rice HP45

text: NCGR

text: public

text: rice HP45

text: rice

text: Oryza sativa

text: Oryza sativa


rice HP48

text: NCGR

text: public

text: rice HP48

text: rice

text: Oryza sativa

text: Oryza sativa


rice HP486

text: NCGR

text: public

text: rice HP486

text: rice

text: Oryza sativa

text: Oryza sativa


rice HP492

text: NCGR

text: public

text: rice HP492

text: rice

text: Oryza sativa

text: Oryza sativa


rice HP577

text: NCGR

text: public

text: rice HP577

text: rice

text: Oryza sativa

text: Oryza sativa


rice HP98

text: NCGR

text: public

text: rice HP98

text: rice

text: Oryza sativa

text: Oryza sativa


rice Nipponbare

text: NCGR

text: public

text: rice Nipponbare

text: rice

text: Oryza sativa

text: Oryza sativa

text: Nipponbare


rice W0128

text: NCGR

text: public

text: rice W0128

text: rice

text: Oryza sativa

text: Oryza sativa


common wild rice W0141

text: NCGR

text: public

text: common wild rice W0141

text: common wild rice

text: Oryza rufipogon

text: Oryza rufipogon


common wild rice W0170

text: NCGR

text: public

text: common wild rice W0170

text: common wild rice

text: Oryza rufipogon

text: Oryza rufipogon


common wild rice W1687

text: NCGR

text: public

text: common wild rice W1687

text: common wild rice

text: Oryza rufipogon

text: Oryza rufipogon


common wild rice W1698

text: NCGR

text: public

text: common wild rice W1698

text: common wild rice

text: Oryza rufipogon

text: Oryza rufipogon


common wild rice W1739

text: NCGR

text: public

text: common wild rice W1739

text: common wild rice

text: Oryza rufipogon

text: Oryza rufipogon


common wild rice W1754

text: NCGR

text: public

text: common wild rice W1754

text: common wild rice

text: Oryza rufipogon

text: Oryza rufipogon


common wild rice W1777

text: NCGR

text: public

text: common wild rice W1777

text: common wild rice

text: Oryza rufipogon

text: Oryza rufipogon


common wild rice W1943

text: NCGR

text: public

text: common wild rice W1943

text: common wild rice

text: Oryza rufipogon

text: Oryza rufipogon


common wild rice W1979

text: NCGR

text: public

text: common wild rice W1979

text: common wild rice

text: Oryza rufipogon

text: Oryza rufipogon


common wild rice W2012

text: NCGR

text: public

text: common wild rice W2012

text: common wild rice

text: Oryza rufipogon

text: Oryza rufipogon


text: UPSC

text: public

text: thale cress

text: Col-0 biological replicate 1 collected after 9 days growth at 16 degrees C

characteristic: description

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: Col-0 biological replicate 2 collected after 9 days growth at 16 degrees C

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: Col-0 biological replicate 3 collected after 9 days growth at 16 degrees C

text: Arabidopsis thaliana

text: Arabidopsis thaliana

characteristic: title


characteristic: External Id

text: UPSC

text: public

text: thale cress

text: Col-0 biological replicate 1 collected after 9 days growth at 23 degrees C

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

characteristic: INSDC center name

text: public

text: thale cress

text: Col-0 biological replicate 2 collected after 9 days growth at 23 degrees C

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

characteristic: INSDC first public

text: public

text: thale cress

text: Col-0 biological replicate 3 collected after 9 days growth at 23 degrees C

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

characteristic: common name

text: Col-0 biological replicate 1 collected after 9 days growth at 16 degrees C followed by 3 days growth at 23 degrees C

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: Col-0 biological replicate 2 collected after 9 days growth at 16 degrees C followed by 3 days growth at 23 degrees C

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: Col-0 biological replicate 3 collected after 9 days growth at 16 degrees C followed by 3 days growth at 23 degrees C

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: Col-0 biological replicate 1 collected after 9 days growth at 23 degrees C followed by 3 days growth at 16 degrees C (experiment A)

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: Col-0 biological replicate 2 collected after 9 days growth at 23 degrees C followed by 3 days growth at 16 degrees C (experiment A)

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: Col-0 biological replicate 3 collected after 9 days growth at 23 degrees C followed by 3 days growth at 16 degrees C (experiment A)

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: Col-0 biological replicate 1 collected after 9 days growth at 23 degrees C followed by 3 days growth at 16 degrees C

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: Col-0 biological replicate 2 collected after 9 days growth at 23 degrees C followed by 3 days growth at 16 degrees C

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: Col-0 biological replicate 3 collected after 9 days growth at 23 degrees C followed by 3 days growth at 16 degrees C

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: Col-0 biological replicate 1 collected after 9 days growth at 23 degrees C followed by 3 days growth at 27 degrees C (experiment A)

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: Col-0 biological replicate 2 collected after 9 days growth at 23 degrees C followed by 3 days growth at 27 degrees C (experiment A)

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: Col-0 biological replicate 3 collected after 9 days growth at 23 degrees C followed by 3 days growth at 27 degrees C (experiment A)

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: Col-0 biological replicate 1 collected after 12 days growth at 23 degrees C (experiment A)

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: Col-0 biological replicate 2 collected after 12 days growth at 23 degrees C (experiment A)

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: Col-0 biological replicate 3 collected after 12 days growth at 23 degrees C (experiment A)

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: pcp mutant biological replicate 1 collected after 9 days growth at 16 degrees C followed by 3 days growth at 23 degrees C rerun

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: pcp mutant biological replicate 1 collected after 9 days growth at 16 degrees C followed by 3 days growth at 23 degrees C

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: pcp mutant biological replicate 2 collected after 9 days growth at 16 degrees C followed by 3 days growth at 23 degrees C rerun

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: pcp mutant biological replicate 2 collected after 9 days growth at 16 degrees C followed by 3 days growth at 23 degrees C

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: pcp mutant biological replicate 3 collected after 9 days growth at 16 degrees C followed by 3 days growth at 23 degrees C

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: pcp mutant biological replicate 1 collected after 9 days growth at 23 degrees C followed by 3 days growth at 16 degrees C

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: pcp mutant biological replicate 2 collected after 9 days growth at 23 degrees C followed by 3 days growth at 16 degrees C

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: pcp mutant biological replicate 3 collected after 9 days growth at 23 degrees C followed by 3 days growth at 16 degrees C

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: pcp mutant biological replicate 1 collected after 9 days growth at 16 degrees C

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: pcp mutant biological replicate 2 collected after 9 days growth at 16 degrees C

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: pcp mutant biological replicate 3 collected after 9 days growth at 16 degrees C

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: pcp mutant biological replicate 1 collected after 9 days growth at 23 degrees C

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: pcp mutant biological replicate 2 collected after 9 days growth at 23 degrees C

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: UPSC

text: public

text: thale cress

text: pcp mutant biological replicate 3 collected after 9 days growth at 23 degrees C

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: Adult

text: Fibrosis

characteristic: ArrayExpress-PHENOTYPE

text: male

characteristic: ArrayExpress-SEX

text: Mus musculus

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: house mouse

text: Male

characteristic: gender

text: Mus musculus

text: Fibrosis

characteristic: phenotype

text: Mus musculus

characteristic: subject id


text: Adult

text: Healthy

text: male

text: Mus musculus

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: house mouse

text: Male

text: Mus musculus

text: Healthy

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: AimiGene

text: public

characteristic: Submitter Id

characteristic: collection date

text: human skin

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: skin

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: metagenomes

text: AD

characteristic: project name

text: metagenomes

text: Illumina

characteristic: sequencing method

text: Skin sample From China


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: AimiGene

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: human oral

text: human-associated habitat

text: oral

text: China

text: human-associated

text: metagenome

text: metagenomes

characteristic: organism

text: AD

text: metagenomes

text: Illumina

text: Oral sample From China

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: AimiGene

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human gut

characteristic: environment (biome)

text: human-associated habitat

text: faeces

text: China

text: human-associated

text: metagenome

text: metagenomes

text: AD

text: metagenomes

text: Illumina

text: Stool sample From China


text: DTU

text: public

text: ArrayExpress

characteristic: broker name

text: Protocols: A serial-passage evolution experiment was performed with the studied strains. Upon each new serial passage (seed), a time-series sample (2 mL culture) was collected and stored at -20 deg. C. according to detailed specifications in manuscript. Seed number thereby refers to the number of passages that the population has been through, each passage was taken after a 16 hour time point. Growth in M9 medium according to manuscript specifications. As described in the manuscript, eight parallel lineages (c1-4 and c6-9) of E coli equipped with a mevalonic acid production pathway were cultured by serial passing. Each new serial passage/seed, (2 % volume) was conducted following 16 hours of cultivation to avoid stationary-phase culture. Nucleic acids extracted by standard plasmid extraction kit (Macharey Nagel) Nextera XT v2 with two extra limited PCR cycles

characteristic: description

text: pe1 (atoB, mvaS, mvaE, araC)

characteristic: genotype

text: M9 medium, 30 degrees celsius

characteristic: growth condition

characteristic: individual

text: Escherichia coli K-12

text: Escherichia coli K-12

characteristic: passage

text: Escherichia coli K-12


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: DTU

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: e3.9 (atoB, mvaS, mvaE, araC, pfolP::pBAD)

text: M9 medium, 30 degrees celsius

text: Escherichia coli K-12

text: Escherichia coli K-12

text: Escherichia coli K-12


characteristic: ENA-CHECKLIST

text: German Centre for Integrative Biodiversity Research (iDiv)

characteristic: INSDC last update

text: public

text: France

characteristic: geographic location (country and/or sea)

text: Malain

characteristic: geographic location (region and locality)

text: Lacerta bilineata

characteristic: organism

text: Lacerta bilineata

text: Female

characteristic: sex

text: Tail muscle

characteristic: tissue type

text: L. bilineata genome Illumina reads

characteristic: title


characteristic: ENA-LAST-UPDATE

text: INSTITUT DE CIENCIES DEL MAR

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:INSTITUT DE CIENCIES DEL MAR

characteristic: Submitter Id

characteristic: collection date

text: uncultured eukaryote

characteristic: common name

text: Sequences from Lake Baikal

characteristic: description

text: Freshwater lake biome

characteristic: environment (biome)

text: lake

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Yes

characteristic: environmental sample

characteristic: further details

text: Russia

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Illumina MiSeq

text: uncultured eukaryote

text: F 5'-CCAGCASCYGCGGTAATTCC-3' R 5'-ACTTTCGTTCTTGATYRA-3'

characteristic: pcr primers

text: uncultured eukaryote

characteristic: size fraction lower threshold

characteristic: size fraction upper threshold

characteristic: target gene

characteristic: target subfragment

text: Lake Baikal


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Universidad de Costa Rica

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Universidad de Costa Rica

characteristic: Submitter Id

text: Carbofuran-degrading consortium obtained by selective enrichment from a pesticide-degrading biomixture

text: bacterium

characteristic: organism

text: bacterium

text: Carbofuran-degrading consortium

characteristic: title


text: NORWEGIAN UNIVERSITY OF LIFE SCIENCES

text: public

tag: Namespace:NORWEGIAN UNIVERSITY OF LIFE SCIENCES

text: Unni Grimholt

characteristic: collected by

text: Atlantic salmon

characteristic: common name

text: Salmo salar

text: Salmo salar

text: Four double haploid Atlantic salmon


text: public

tag: Namespace:KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY

characteristic: collection date

text: Pool of 3 Replicates

characteristic: description

text: sea

characteristic: environment (biome)

text: coast

characteristic: environment (feature)

text: seawater

characteristic: environment (material)

text: Greece

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: seawater metagenome

text: Aquanano

characteristic: project name

text: seawater metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: Control day 0

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

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text: Pool of 3 Replicates

text: sea

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text: seawater

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text: metagenome

text: seawater metagenome

characteristic: organism

text: Aquanano

text: seawater metagenome

text: Illumina MiSeq

text: Silver Nanoparticle Treatment day 0

text: water


text: public

characteristic: collection date

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text: metagenome

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text: Illumina MiSeq

text: Control day 5

characteristic: title

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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characteristic: External Id

text: public

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characteristic: geographic location (longitude)

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text: Replicate 3

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text: sea

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text: metagenome

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characteristic: organism

text: Aquanano

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text: Illumina MiSeq

text: Control day 5

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characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: Replicate 1

text: sea

characteristic: environment (biome)

text: coast

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text: seawater

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text: Greece

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metagenome

text: seawater metagenome

text: Aquanano

text: seawater metagenome

text: Illumina MiSeq

text: Silver Nanoparticle Treatment day 5

characteristic: title

text: water


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Replicate 2

text: sea

text: coast

text: seawater

text: Greece

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: seawater metagenome

text: Aquanano

characteristic: project name

text: seawater metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: Silver Nanoparticle Treatment day 5

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characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

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text: Replicate 3

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text: sea

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text: metagenome

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characteristic: organism

text: Aquanano

text: seawater metagenome

text: Illumina MiSeq

text: Silver Nanoparticle Treatment day 5

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characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Replicate 1

text: sea

characteristic: environment (biome)

text: coast

characteristic: environment (feature)

text: seawater

characteristic: environment (material)

text: Greece

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metagenome

text: seawater metagenome

text: Aquanano

text: seawater metagenome

text: Illumina MiSeq

text: Control day 11

characteristic: title

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Replicate 2

text: sea

text: coast

text: seawater

text: Greece

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: seawater metagenome

text: Aquanano

characteristic: project name

text: seawater metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: Control day 11

text: water

characteristic: water environmental package


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Replicate 3

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text: sea

text: coast

text: seawater

text: Greece

text: metagenome

text: seawater metagenome

characteristic: organism

text: Aquanano

text: seawater metagenome

text: Illumina MiSeq

text: Control day 11

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: Replicate 1

text: sea

characteristic: environment (biome)

text: coast

characteristic: environment (feature)

text: seawater

characteristic: environment (material)

text: Greece

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metagenome

text: seawater metagenome

text: Aquanano

text: seawater metagenome

text: Illumina MiSeq

text: Silver Nanoparticle Treatment day 11

characteristic: title

text: water


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Replicate 2

text: sea

text: coast

text: seawater

text: Greece

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: seawater metagenome

text: Aquanano

characteristic: project name

text: seawater metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: Silver Nanoparticle Treatment day 11

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Replicate 3

characteristic: description

text: sea

text: coast

text: seawater

text: Greece

text: metagenome

text: seawater metagenome

characteristic: organism

text: Aquanano

text: seawater metagenome

text: Illumina MiSeq

text: Silver Nanoparticle Treatment day 11

text: water


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Replicate 1

text: sea

characteristic: environment (biome)

text: coast

characteristic: environment (feature)

text: seawater

characteristic: environment (material)

text: Greece

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metagenome

text: seawater metagenome

text: Aquanano

text: seawater metagenome

text: Illumina MiSeq

text: Control day 25

characteristic: title

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Replicate 2

text: sea

text: coast

text: seawater

text: Greece

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: seawater metagenome

text: Aquanano

characteristic: project name

text: seawater metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: Control day 25

text: water

characteristic: water environmental package


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Replicate 1

characteristic: description

text: sea

text: coast

text: seawater

text: Greece

text: metagenome

text: seawater metagenome

characteristic: organism

text: Aquanano

text: seawater metagenome

text: Illumina MiSeq

text: Silver Nanoparticle Treatment day 25

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: Replicate 2

text: sea

characteristic: environment (biome)

text: coast

characteristic: environment (feature)

text: seawater

characteristic: environment (material)

text: Greece

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metagenome

text: seawater metagenome

text: Aquanano

text: seawater metagenome

text: Illumina MiSeq

text: Silver Nanoparticle Treatment day 25

characteristic: title

text: water


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Replicate 1

text: sea

text: coast

text: seawater

text: Greece

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: seawater metagenome

text: Aquanano

characteristic: project name

text: seawater metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: Control day 32

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Replicate 2

characteristic: description

text: sea

text: coast

text: seawater

text: Greece

text: metagenome

text: seawater metagenome

characteristic: organism

text: Aquanano

text: seawater metagenome

text: Illumina MiSeq

text: Control day 32

text: water


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Replicate 1

text: sea

characteristic: environment (biome)

text: coast

characteristic: environment (feature)

text: seawater

characteristic: environment (material)

text: Greece

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metagenome

text: seawater metagenome

text: Aquanano

text: seawater metagenome

text: Illumina MiSeq

text: Silver Nanoparticle Treatment day 32

characteristic: title

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Replicate 2

text: sea

text: coast

text: seawater

text: Greece

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: seawater metagenome

text: Aquanano

characteristic: project name

text: seawater metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: Silver Nanoparticle Treatment day 32

text: water

characteristic: water environmental package


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF KIEL

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:UNIVERSITY OF KIEL

characteristic: Submitter Id

text: house mouse

characteristic: common name

characteristic: description

text: Mus musculus

characteristic: organism

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: TUM

text: public

text: human

text: Fecal sample from an IBS patient following a FODMAP diet

text: FODMAP

characteristic: group

text: Homo sapiens

text: Homo sapiens

characteristic: time

text: Yoga-IBS

characteristic: title


text: TUM

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human

text: Fecal sample from an IBS patient following a Yoga course

text: Yoga

text: Homo sapiens

text: Homo sapiens

text: Yoga-IBS


text: European Robin

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: European robin

text: Erithacus rubecula

text: Erithacus rubecula

characteristic: subject id

text: Erithacus rubecula


Enrichment culture A

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Enrichment culture A

tag: Namespace:HELMHOLTZ CENTRE FOR ENVIRONMENTAL RESEARCH - UFZ

text: bacterium

text: bacterium

text: Acesulfame-degrading bacteria enriched from a wetland treating municipal wastewater


Enrichment culture B

text: HELMHOLTZ CENTRE FOR ENVIRONMENTAL RESEARCH - UFZ

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Enrichment culture B

text: bacterium

text: bacterium


Enrichment culture C

text: public

characteristic: SRA accession

text: Enrichment culture C

characteristic: Submitter Id

text: bacterium

text: bacterium


Enrichment culture 1a

text: public

text: Enrichment culture 1a

text: bacterium

text: bacterium


Enrichment culture 2c

text: public

text: Enrichment culture 2c

text: bacterium

text: bacterium


Enrichment culture 3b

text: public

text: Enrichment culture 3b

text: bacterium

text: bacterium


Enrichment culture I

text: public

text: Enrichment culture I

text: bacterium

text: bacterium


Enrichment culture II

text: public

text: Enrichment culture II

text: bacterium

text: bacterium


Enrichment culture III

text: public

text: Enrichment culture III

text: bacterium

text: bacterium


Enrichment culture IV

text: public

text: Enrichment culture IV

text: bacterium

text: bacterium


E-MTAB-6362:Sample 1

text: KIS

text: public

text: E-MTAB-6362:Sample 1

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

text: house mouse

characteristic: common name

text: Protocols: The mESCs (129/CAST) with and without a CRISPR- induced deletion of the Sox2 super-enhancer on the CAST allele was constructed in the Bing Ren lab[Ref 1]. Single cells of the 129/CAST cross (wild type) and with the Sox2 enhancer deletion on the CAST allele was grown as described[Ref 2] and later FACS sorted with BD Influx cell sorter (BD Biosciences) individually into 384-well plates containing 2.3 ul of the single-cell RNA-seq lysis buffer. Plates were immediately frozen until further processed. Ref 1: Li, Y. et al. CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells. PLoS ONE 9, e114485 (2014). Ref 2: Supplemental Methods_nov20 Selvaraj, S., R Dixon, J., Bansal, V. & Ren, B. Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing. Nat. Biotechnol. 31, 1111-1118 (2013). Smart-seq2, indexed by Nextera i5 and i7 indices. We used ERCC spike-in RNA (Thermo Fischer Scientific, cat no. 4456740).

characteristic: description

text: embryo

characteristic: developmental stage

text: heterozygous deletion of sox2 superenhancer (CAST allele)

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: inner cell mass

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

text: 129SvEv x CAST/EiJ

characteristic: strain

text: Sample 1


E-MTAB-6362:Sample 10

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: KIS

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-6362:Sample 10

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: embryo

text: Mus musculus

characteristic: organism

text: Mus musculus

text: inner cell mass

text: Mus musculus

text: male

text: 129SvEv x CAST/EiJ

text: Sample 10

characteristic: title


E-MTAB-6362:Sample 100

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: KIS

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6362:Sample 100

characteristic: Submitter Id

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: embryo

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: Mus musculus

text: male

text: 129SvEv x CAST/EiJ

text: Sample 100


E-MTAB-6362:Sample 101

text: KIS

text: public

text: E-MTAB-6362:Sample 101

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

text: embryo

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: Mus musculus

text: male

text: 129SvEv x CAST/EiJ

text: Sample 101


E-MTAB-6362:Sample 102

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: KIS

text: public

text: E-MTAB-6362:Sample 102

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: embryo

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: inner cell mass

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

text: 129SvEv x CAST/EiJ

characteristic: strain

text: Sample 102


E-MTAB-6362:Sample 103

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: KIS

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-6362:Sample 103

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: embryo

text: Mus musculus

characteristic: organism

text: Mus musculus

text: inner cell mass

text: Mus musculus

text: male

text: 129SvEv x CAST/EiJ

text: Sample 103

characteristic: title


E-MTAB-6362:Sample 104

text: KIS

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6362:Sample 104

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: embryonic stem cell

text: house mouse

text: embryo

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: Mus musculus

text: male

text: 129SvEv x CAST/EiJ

text: Sample 104


E-MTAB-6362:Sample 105

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: KIS

text: public

text: E-MTAB-6362:Sample 105

text: ArrayExpress

text: embryonic stem cell

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

text: embryo

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: Mus musculus

text: male

text: 129SvEv x CAST/EiJ

text: Sample 105


E-MTAB-6362:Sample 106

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: KIS

text: public

text: E-MTAB-6362:Sample 106

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: embryo

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: inner cell mass

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

text: 129SvEv x CAST/EiJ

characteristic: strain

text: Sample 106


E-MTAB-6362:Sample 107

text: KIS

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-6362:Sample 107

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: embryo

text: Mus musculus

characteristic: organism

text: Mus musculus

text: inner cell mass

text: Mus musculus

text: male

text: 129SvEv x CAST/EiJ

text: Sample 107

characteristic: title