name: E-MTAB-49181491395130:mitotic nuclear cycle 1-14 repl 1

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:Max Planck Institute for Molecular Biomedicine

text: ArrayExpress

text: M-phase

characteristic: cell cycle phase

text: fruit fly

text: Protocols: Following a pre-collection period of at least one hour, fly embryos were collected on yeasted 0.4% acetic acid agar plates at 25°C. After 30 min of collection, the embryos on the plate were incubated at 25°C until they reached the desired developmental stage. Embryos were dechorionated for 2 min in 2.5% sodium hypochlorite and rinsed with water. Sorting was carried out on ice in PBS, 0.5% Triton X-100 including cOmplete Ultra protease inhibitors (Roche). We sorted embryos in small batches of approximately 100 embryos at a time under a Leica X fluorescent binocular equipped with a GFP filter set. We used the fluorescent signal from the PCNA-eGFP transgene to determine the developmental stage and cell cycle status of each embryo. The developmental stage was readily established by examining the nuclear density, which roughly doubles with each nuclear division cycle. Embryos undergoing a mitotic division cycle were easily identifiable by the lack of nuclear PCNA-eGFP signal. Embryos for stage 7-8 were sorted solely based on their morphology. We removed all embryos with inappropriate developmental stage or mitotic nuclei as well as damaged embryos or such with abnormal morphology. The remaining sorted population of embryos was imaged for quality control. Using this sorting procedure, we obtained >99.9% nuclear-cycle specific populations of embryos for our experiments. Embryos were suspended in 2 ml of PBS, 0.5% Triton X-100 and 6 ml of heptane. Cross-linking was initiated by adding 100 μl of 37% formaldehyde, followed by vigorous shaking. 10 min later, samples were spun at 500 g for 1 min and embryos were collected from the lower aqueous layer. 15 min after the start of fixation, 5 ml of PBS, 0.5% Triton X-100, 125 mM glycine was added to the embryos, followed by vigorous shaking for 1 min. The embryos were rinsed 3 times with PBS, 0.5% Triton X-100. We followed the general procedure for in situ Hi-C as described in Rao et al. (doi: 10.1016/j.cell.2014.11.021), which we adapted for use with fly embryos. The frozen embryos were placed on ice and suspended in 500 μl of ice-cold lysis buffer (10 mM Tris-Cl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630, cOmplete Ultra protease inhibitors). Using a tight-fitting metal pestle (Carl-Roth P985.1) the embryos were ground until a homogenous suspension was achieved. After 15 min incubation on ice, the nuclei were spun down at 1000 g, 4°C for 5 min. The supernatant was removed and the nuclei pellet resuspended in 500 μl of lysis buffer. Following another spin, the supernatant was discarded and the pellet resuspended in 100 μl 0.5% SDS. The nuclei were permeabilised by incubating at 65°C for 10 min. The SDS was then quenched by adding 50 μl of 10% Triton TX-100 and incubating at 37°C for 15 min. Chromatin was digested by adding 25 μl of CutSmart buffer and 50 U of MboI (New England Biolabs), followed by three hours of incubation at 37°C. The enzyme was added in two instalments of 25 U in the beginning and after 90 min of incubation. MboI was heat-inactivated by incubating at 62°C for 20 min. The overhangs left by MboI were filled in by adding 18.75 μl of 0.4 mM biotin-14-dATP (Life Technologies), 2.25 μl of a 3.3 mM dCTP/dGTP/dTTP mixture and 40 U of DNA Polymerase I Klenow Fragment (New England Biolabs), followed by incubation at 37°C for 90 min. The DNA fragments were then ligated by adding 657 μl of water, 120 μl of 10x T4 DNA Ligase buffer (Thermo Fisher Scientific), 100 μl of 10% Triton X-100, 6 μl of 20 mg/ml BSA and 25 Weiss U of T4 DNA Ligase (Thermo Fisher Scientific). The mixture was rotated slowly at room temperature for four hours. A second instalment of 25 Weiss U of T4 DNA Ligase was added after two hours. The nuclei were then spun down at 2500 g for 5 min, the supernatant discarded and the pellet resuspended in 500 μl of extraction buffer (50 mM Tris-Cl pH 8.0, 50 mM NaCl, 1 mM EDTA, 1% SDS). To digest the protein, 20 μl of 20 mg/ml Proteinase K (Applichem) was added and the mixture incubated at 55°C, 1000 rpm shaking for 30 min. 130 μl of 5 M sodium chloride was added and the mixture was incubated at 68°C, 1000 rpm shaking for at least 8 hours. For DNA precipitation, 63 μl of 3 M sodium acetate pH 5.2, 2 μl of 15 mg/ml GlycoBlue (Life Technologies) and finally 1008 μl of absolute ethanol were mixed with the sample, followed by incubation at -80°C for 15 min. The sample was then spun at 20,000 g, 4°C for one hour. The supernatant was removed and the DNA pellet washed two times using 800 μl of 70% ethanol each. All traces of remaining supernatant were removed; the pellet air-dried for 2 min and then solubilized in 50 μl of 10 mM Tris-Cl pH 8.0. RNA was digested by adding 1 μl of 20 mg/ml RNase A and incubating at 37°C for 15 min. Biotin-14-dATP was removed from the ends of unligated fragments by mixing 50 μl of the Hi-C library with 12 μl of 10x NEB2 buffer (New England Biolabs), 3 μl of 1 mM dATP, 3 μl of 1 mM dGTP, 0.6 μl of 20 mg/ml BSA, 15 U of T4 DNA Polymerase (New England Biolabs) and water to 120 μl total. The mixture was incubated at 20°C for 30 min and then stopped by adding 3 μl of 0.5 M EDTA. The DNA was sheared to ~200-400 bp with a Covaris S2 sonicator using the following program: 2 cycles á 50 seconds, 10% duty, intensity 5, 200 cycles/burst. For the preparation of magnetic beads for biotin pull-down, 30 μl of Dynabeads MyOne Streptavidin C1 (Life Technologies) were separated on a magnetic stand. The supernatant was discarded. The beads were washed once and then resuspended in 120 μl of 1x B&W buffer (2x stock: 10 mM Tris-Cl pH 7.4, 1 mM EDTA, 2 M NaCl). 120 μl of the sheared Hi-C sample was mixed with 120 μl of the prepared magnetic beads and the suspension was rotated at room temperature for 15 min. The beads were washed twice with 600 μl each of 1x B&W buffer + 0.1% Triton X-100 by incubating at 55°C, 1000 rpm shaking for 2 min. This was followed by a wash with 10 mM Tris-Cl pH 8.0. The beads were then resuspended in 50 μl of the same solution. Next, library preparation for Illumina sequencing was performed using components from the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs). 3 μl of End Prep Enzyme Mix and 7 μl of End Prep Reaction buffer were combined in a 0.2 ml PCR strip tube. The bead suspension in 50 μl Tris-Cl pH 8.0 was mixed into the End Prep mixture and incubated in a thermocycler running the following program: 20°C for 30 min, 65°C for 30 min, 4°C hold. 30 μl of Ligation Master Mix, 2.5 μl Adaptor for Illumina (1:10 diluted from stock) and 1 μl of Ligation enhancer were added to the sample and the mixture was incubated in a thermocycler at 20°C for 15 min. Next, 3 μl of USER enzyme was added and the mixture incubated at 37°C for 15 min in a thermocycler. The beads were separated on a magnetic stand and the supernatant was discarded. The beads were washed twice using 1x B&W + 0.1% Triton X-100 and transferred to a 1.5 ml tube. The beads containing the final adapter-ligated Hi-C library were washed once with 10 mM Tris-Cl pH 8.0 and then resuspended in 50 μl of the same solution.

text: nuclear cycle 1-14

characteristic: developmental stage

text: wild type

characteristic: genetic modification

text: w[*]; P{EGFP-PCNA}attP2

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: mitotic nuclear cycle 1-14 repl 1


name: E-MTAB-49181491395130:mitotic nuclear cycle 1-14 repl 2

status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Max Planck Institute for Molecular Biomedicine

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: M-phase

text: fruit fly

characteristic: common name

characteristic: description

text: nuclear cycle 1-14

text: wild type

text: w[*]; P{EGFP-PCNA}attP2

characteristic: genotype

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

text: mitotic nuclear cycle 1-14 repl 2

characteristic: title


name: E-MTAB-49181491395130:nuclear cycle 14 alpha-amanitin injected ChIP input repl 1

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: S-phase

characteristic: cell cycle phase

text: fruit fly

text: Protocols: Following a pre-collection period of at least one hour, fly embryos were collected on yeasted 0.4% acetic acid agar plates at 25°C. After 30 min of collection, the embryos on the plate were incubated at 25°C until they reached the desired developmental stage. Embryos were dechorionated for 2 min in 2.5% sodium hypochlorite and rinsed with water. Embryos were suspended in 2 ml of PBS, 0.5% Triton X-100 and 6 ml of heptane. Cross-linking was initiated by adding 100 μl of 37% formaldehyde, followed by vigorous shaking. 10 min later, samples were spun at 500 g for 1 min and embryos were collected from the lower aqueous layer. 15 min after the start of fixation, 5 ml of PBS, 0.5% Triton X-100, 125 mM glycine was added to the embryos, followed by vigorous shaking for 1 min. The embryos were rinsed 3 times with PBS, 0.5% Triton X-100. Crosslinking and chromatin preparation from nuclear cycle 14 embryos was carried out as described in (Blythe and Wieschaus, 2015). After injection and storage at -80°C, 150 to 200 embryos where mechanically homogenized in 700 μl of RIPA (150 mM NaCl, 1.0% IGEPAL® CA-630, 0.5% sodium deoxycholate, 0.1% SDS, 50 mM Tris, pH 8.0) + protease inhibitors (Sigma 04693159001) using a pellet pestle. After centrifugation for 5 min at 16000 g and 4°C, the supernatant was discarded taking care of pipetting out lipids at the surface and not touching the pellet. The pellet was then resuspended in 130 μl of fresh RIPA + protease inhibitors and sonicated on a Covaris S2 sonicator at 5% duty cycle for 10 minutes. Following sonication, the samples were centrifuged at 16000 g for 5 min at 4°C. The supernatant (~ 120 μl), containing the chromatin, was finally carefully removed and split in 2x 50 μl aliquots. The remaining 20 μl were decrosslinked overnight at 61°C with proteinase K 1 mg/ml final and loaded on a 1.5% agarose gel with 1X GelRed (Biotium #41003), migrated for 1.5 hours at 65V, and imaged to control that the size of the fragments was between 150 and 500 bp. During the whole procedure, the samples were constantly kept on ice to minimize protein degradation. Chromatin immunoprecipitation was performed using commercial kits (17-10085 Millipore) in 1.5 ml DNA LoBind Eppendorf tubes (Eppendorf) as follows. For each ChIP, 450 μl of dilution buffer was supplemented with 2.25 μl of protease inhibitor cocktail, and added to a 50 μl chromatin aliquot. For each sample, 5 μl (corresponding to 1% of the total volume) is set apart and stored at 4°C for later processing. These aliquot contain non-immunoprecipitated chromatin, which will serve as input during the processing of the ChIP-Seq and the analysis of the qPCR. To each 500 μl reaction volume, 20 μl of magnetic beads were added. The antibodies (anti-RNA Pol II pSer5: ab5408, Abcam; anti-pan RNA Pol II: ab103968, Abcam) were respectively used at a final dilution of 6:1000 and 18:1000 (3 μl or 9 μl in a 500 μl volume, respectively). The samples were then incubated overnight at 4°C on a rotating wheel. The next day, the beads were washed twice with the low salt buffer, twice with the high salt buffer, once with the LiCl buffer, and once with TE. These more stringent washes allow for better ChIP enrichment. Both the beads and the 5 μl previously set aside were finally resuspended in 100 μl of elution buffer + proteinase K 1 mg / ml final and incubated overnight at 61°C. The following day, the volume of the samples were adjusted to 400 μl with TE and DNA purified with an equal volume of phenol:chloroform:isoamyl alcohol 25:24:1 (Sigma) in a phase-lock-gel tube (5prime). After centrifugation at 12000 g for 5 min at RT, the supernatant (400 μl) was transferred to a new tube. The DNA was precipitated by addition of 40 μl of sodium acetate 3M pH 5, 2 μl of glycogen 20 mg/ml and 640 ml of -20°C ethanol 100%. The samples were then incubated for 1h at -20°C and centrifuged at 16000 g for 5 min at 4°C. Finally, the DNA pellets were washed twice with 800 μl -20°C ethanol 70% and resuspended in 20 μl TE. ChIP-Seq libraries were prepared directly from immunoprecipitated material using NEBNext Ultra II DNA Library Prep Kits (E7645, NEB) as follows. The immunoprecipitated material volume was adjusted to 50 μl with Tris-Cl pH 8.0 and transferred to a 0.2 ml PCR strip tube. To the reaction volume, 3 μl of End Prep Enzyme Mix and 7 μl of End Prep Reaction buffer were added. The mixture was incubated in a thermocycler running the following program: 20°C for 30 min, 65°C for 30 min, 4°C hold. 30 μl of Ligation Master Mix, 2.5 μl Adaptor for Illumina (1:15 diluted from stock) and 1 μl of Ligation enhancer were added to the sample and the mixture was incubated in a thermocycler at 20°C for 15 min. Next, 3 μl of USER enzyme was added and the mixture incubated at 37°C for 15 min in a thermocycler. Because of the low amount of initial material (2-5 ng), as recommended by the manufacturer, a size-selection step was not performed and fragments were cleaned up to eliminate unligated adaptors by adding 87 μl of Ampure XP beads (Agencourt) and mixing it with the reaction volume. After a 5 min incubation at RT, the beads were separated on a magnetic stand and the supernatant containing the short fragments was discarded. The beads were then washed twice with 200 μl of ethanol 80%, air dried for 5 min and resuspended in 15 μl of Tris-Cl pH 8.0. After separating the beads on a magnetic stand, the supernatant was transferred to a new 0.2 ml PCR. For each library, a PCR reaction was prepared as follows: 25 μl of 2x NEBNext Ultra II Q5 Master Mix, 5 μl of 25 μM Universal PCR primer, 5 μl of 25 μM Indexed PCR primer and finally 15 μl of the ChIP-Seq library. The PCR reactions were run using the following program: 98°C for 30 sec, (98°C for 10 s, 65°C for 75 s, ramping 1.5°C/s) repeated 12 times, 65°C for 5 min, 4°C hold. The PCR product was size-selected using Ampure XP beads (Beckman Coulter). The PCR reactions were combined and adjusted to exactly 110 μl volume with water. 110 μl of beads were mixed with the sample and incubated at room temperature for 5 min. After separation on a magnetic stand, the supernatant was moved to a new tube and the beads discarded. Another 40 μl of beads was added to the sample and incubated at room temperature for 5 min. After separation, the supernatant was discarded and the beads washed twice with 700 μl of 80% ethanol, each time incubating for 30 seconds. Following complete removal of the ethanol, the beads were resuspended in 100 μl of 10 mM Tris-Cl pH 8.0 and incubated at room temperature for 1 min. The following second round of selection removes all traces of primers and possible primer dimers. Without separating, another 80 μl of fresh beads was added and the suspension was incubated at room temperature for 5 min. After separation of the beads, the supernatant was discarded and the beads were washed twice with 80% ethanol, as above. After all traces of ethanol were removed, the beads were resuspended in 20 μl of 10 mM Tris-Cl pH 8.0 and incubated at RT for 5 min. Finally, the supernatant, containing the final library was transferred to a 1.5 ml DNA LoBind Eppendorf tube.

text: nuclear cycle 14

characteristic: developmental stage

text: wild type

text: w[*]; P{EGFP-PCNA}attP2

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed


name: E-MTAB-49181491395130:nuclear cycle 14 alpha-amanitin injected ChIP input repl 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: S-phase

text: fruit fly

text: nuclear cycle 14

text: wild type

characteristic: genetic modification

text: w[*]; P{EGFP-PCNA}attP2

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

characteristic: sex


name: E-MTAB-49181491395130:nuclear cycle 14 alpha-amanitin injected ChIP Pol II pan repl 1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: S-phase

text: fruit fly

text: nuclear cycle 14

text: wild type

text: w[*]; P{EGFP-PCNA}attP2

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed


name: E-MTAB-49181491395130:nuclear cycle 14 alpha-amanitin injected ChIP Pol II pan repl 2

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: S-phase

text: fruit fly

characteristic: common name

text: nuclear cycle 14

text: wild type

text: w[*]; P{EGFP-PCNA}attP2

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed


name: E-MTAB-49181491395130:nuclear cycle 14 alpha-amanitin injected ChIP Pol II ser5p repl 1

text: public

text: ArrayExpress

text: S-phase

text: fruit fly

characteristic: description

text: nuclear cycle 14

text: wild type

text: w[*]; P{EGFP-PCNA}attP2

characteristic: genotype

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

characteristic: title


name: E-MTAB-49181491395130:nuclear cycle 14 alpha-amanitin injected ChIP Pol II ser5p repl 2

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: S-phase

characteristic: cell cycle phase

text: fruit fly

text: nuclear cycle 14

characteristic: developmental stage

text: wild type

text: w[*]; P{EGFP-PCNA}attP2

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed


name: E-MTAB-49181491395130:nuclear cycle 14 ChIP input repl 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: S-phase

text: fruit fly

text: nuclear cycle 14

text: wild type

characteristic: genetic modification

text: w[*]; P{EGFP-PCNA}attP2

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: nuclear cycle 14 ChIP input repl 1


name: E-MTAB-49181491395130:nuclear cycle 14 ChIP input repl 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: S-phase

text: fruit fly

text: nuclear cycle 14

text: wild type

text: w[*]; P{EGFP-PCNA}attP2

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

text: nuclear cycle 14 ChIP input repl 2


name: E-MTAB-49181491395130:nuclear cycle 14 ChIP Pol II pan repl 1

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: S-phase

text: fruit fly

characteristic: common name

text: nuclear cycle 14

text: wild type

text: w[*]; P{EGFP-PCNA}attP2

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

text: nuclear cycle 14 ChIP Pol II pan repl 1


name: E-MTAB-49181491395130:nuclear cycle 14 ChIP Pol II pan repl 2

text: public

text: ArrayExpress

text: S-phase

text: fruit fly

characteristic: description

text: nuclear cycle 14

text: wild type

text: w[*]; P{EGFP-PCNA}attP2

characteristic: genotype

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

text: nuclear cycle 14 ChIP Pol II pan repl 2

characteristic: title


name: E-MTAB-49181491395130:nuclear cycle 14 ChIP Pol II ser5p repl 1

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: S-phase

characteristic: cell cycle phase

text: fruit fly

text: nuclear cycle 14

characteristic: developmental stage

text: wild type

text: w[*]; P{EGFP-PCNA}attP2

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed


name: E-MTAB-49181491395130:nuclear cycle 14 ChIP Pol II ser5p repl 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: S-phase

text: fruit fly

text: nuclear cycle 14

text: wild type

characteristic: genetic modification

text: w[*]; P{EGFP-PCNA}attP2

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

characteristic: sex


name: E-MTAB-49181491395130:nuclear cycle 14 sh zld repl 1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: S-phase

text: fruit fly

text: Protocols: Following a pre-collection period of at least one hour, fly embryos were collected on yeasted 0.4% acetic acid agar plates at 25°C. After 30 min of collection, the embryos on the plate were incubated at 25°C until they reached the desired developmental stage. Embryos were dechorionated for 2 min in 2.5% sodium hypochlorite and rinsed with water. Embryos were suspended in 2 ml of PBS, 0.5% Triton X-100 and 6 ml of heptane. Cross-linking was initiated by adding 100 μl of 37% formaldehyde, followed by vigorous shaking. 10 min later, samples were spun at 500 g for 1 min and embryos were collected from the lower aqueous layer. 15 min after the start of fixation, 5 ml of PBS, 0.5% Triton X-100, 125 mM glycine was added to the embryos, followed by vigorous shaking for 1 min. The embryos were rinsed 3 times with PBS, 0.5% Triton X-100. We followed the general procedure for in situ Hi-C as described in Rao et al. (doi: 10.1016/j.cell.2014.11.021), which we adapted for use with fly embryos. The frozen embryos were placed on ice and suspended in 500 μl of ice-cold lysis buffer (10 mM Tris-Cl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630, cOmplete Ultra protease inhibitors). Using a tight-fitting metal pestle (Carl-Roth P985.1) the embryos were ground until a homogenous suspension was achieved. After 15 min incubation on ice, the nuclei were spun down at 1000 g, 4°C for 5 min. The supernatant was removed and the nuclei pellet resuspended in 500 μl of lysis buffer. Following another spin, the supernatant was discarded and the pellet resuspended in 100 μl 0.5% SDS. The nuclei were permeabilised by incubating at 65°C for 10 min. The SDS was then quenched by adding 50 μl of 10% Triton TX-100 and incubating at 37°C for 15 min. Chromatin was digested by adding 25 μl of CutSmart buffer and 50 U of MboI (New England Biolabs), followed by three hours of incubation at 37°C. The enzyme was added in two instalments of 25 U in the beginning and after 90 min of incubation. MboI was heat-inactivated by incubating at 62°C for 20 min. The overhangs left by MboI were filled in by adding 18.75 μl of 0.4 mM biotin-14-dATP (Life Technologies), 2.25 μl of a 3.3 mM dCTP/dGTP/dTTP mixture and 40 U of DNA Polymerase I Klenow Fragment (New England Biolabs), followed by incubation at 37°C for 90 min. The DNA fragments were then ligated by adding 657 μl of water, 120 μl of 10x T4 DNA Ligase buffer (Thermo Fisher Scientific), 100 μl of 10% Triton X-100, 6 μl of 20 mg/ml BSA and 25 Weiss U of T4 DNA Ligase (Thermo Fisher Scientific). The mixture was rotated slowly at room temperature for four hours. A second instalment of 25 Weiss U of T4 DNA Ligase was added after two hours. The nuclei were then spun down at 2500 g for 5 min, the supernatant discarded and the pellet resuspended in 500 μl of extraction buffer (50 mM Tris-Cl pH 8.0, 50 mM NaCl, 1 mM EDTA, 1% SDS). To digest the protein, 20 μl of 20 mg/ml Proteinase K (Applichem) was added and the mixture incubated at 55°C, 1000 rpm shaking for 30 min. 130 μl of 5 M sodium chloride was added and the mixture was incubated at 68°C, 1000 rpm shaking for at least 8 hours. For DNA precipitation, 63 μl of 3 M sodium acetate pH 5.2, 2 μl of 15 mg/ml GlycoBlue (Life Technologies) and finally 1008 μl of absolute ethanol were mixed with the sample, followed by incubation at -80°C for 15 min. The sample was then spun at 20,000 g, 4°C for one hour. The supernatant was removed and the DNA pellet washed two times using 800 μl of 70% ethanol each. All traces of remaining supernatant were removed; the pellet air-dried for 2 min and then solubilized in 50 μl of 10 mM Tris-Cl pH 8.0. RNA was digested by adding 1 μl of 20 mg/ml RNase A and incubating at 37°C for 15 min. Biotin-14-dATP was removed from the ends of unligated fragments by mixing 50 μl of the Hi-C library with 12 μl of 10x NEB2 buffer (New England Biolabs), 3 μl of 1 mM dATP, 3 μl of 1 mM dGTP, 0.6 μl of 20 mg/ml BSA, 15 U of T4 DNA Polymerase (New England Biolabs) and water to 120 μl total. The mixture was incubated at 20°C for 30 min and then stopped by adding 3 μl of 0.5 M EDTA. The DNA was sheared to ~200-400 bp with a Covaris S2 sonicator using the following program: 2 cycles á 50 seconds, 10% duty, intensity 5, 200 cycles/burst. For the preparation of magnetic beads for biotin pull-down, 30 μl of Dynabeads MyOne Streptavidin C1 (Life Technologies) were separated on a magnetic stand. The supernatant was discarded. The beads were washed once and then resuspended in 120 μl of 1x B&W buffer (2x stock: 10 mM Tris-Cl pH 7.4, 1 mM EDTA, 2 M NaCl). 120 μl of the sheared Hi-C sample was mixed with 120 μl of the prepared magnetic beads and the suspension was rotated at room temperature for 15 min. The beads were washed twice with 600 μl each of 1x B&W buffer + 0.1% Triton X-100 by incubating at 55°C, 1000 rpm shaking for 2 min. This was followed by a wash with 10 mM Tris-Cl pH 8.0. The beads were then resuspended in 50 μl of the same solution. Next, library preparation for Illumina sequencing was performed using components from the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs). 3 μl of End Prep Enzyme Mix and 7 μl of End Prep Reaction buffer were combined in a 0.2 ml PCR strip tube. The bead suspension in 50 μl Tris-Cl pH 8.0 was mixed into the End Prep mixture and incubated in a thermocycler running the following program: 20°C for 30 min, 65°C for 30 min, 4°C hold. 30 μl of Ligation Master Mix, 2.5 μl Adaptor for Illumina (1:10 diluted from stock) and 1 μl of Ligation enhancer were added to the sample and the mixture was incubated in a thermocycler at 20°C for 15 min. Next, 3 μl of USER enzyme was added and the mixture incubated at 37°C for 15 min in a thermocycler. The beads were separated on a magnetic stand and the supernatant was discarded. The beads were washed twice using 1x B&W + 0.1% Triton X-100 and transferred to a 1.5 ml tube. The beads containing the final adapter-ligated Hi-C library were washed once with 10 mM Tris-Cl pH 8.0 and then resuspended in 50 μl of the same solution.

text: nuclear cycle 14

text: sh zld

text: P{otu-GAL4::VP16.R}1, w[*]; P{GAL4-nos.NGT}40/P{UAS-shRNA-zld}; P{ GAL4::VP16-nos.UTR}CG6325

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

text: nuclear cycle 14 sh zld repl 1


name: E-MTAB-49181491395130:nuclear cycle 14 sh zld repl 2

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: S-phase

text: fruit fly

characteristic: common name

text: nuclear cycle 14

text: sh zld

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

text: nuclear cycle 14 sh zld repl 2


name: E-MTAB-49181491395130:nuclear cycle 14 sh zld repl 3

text: public

text: ArrayExpress

text: S-phase

text: fruit fly

characteristic: description

text: nuclear cycle 14

text: sh zld

characteristic: genotype

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

text: nuclear cycle 14 sh zld repl 3

characteristic: title


name: E-MTAB-49181491395130:nuclear cycle 14 sh zld repl 4

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: S-phase

characteristic: cell cycle phase

text: fruit fly

text: nuclear cycle 14

characteristic: developmental stage

text: sh zld

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

text: nuclear cycle 14 sh zld repl 4


name: E-MTAB-49181491395130:nuclear cycle 14 triptolide injected ChIP input repl 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: S-phase

text: fruit fly

text: nuclear cycle 14

text: wild type

characteristic: genetic modification

text: w[*]; P{EGFP-PCNA}attP2

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

characteristic: sex


name: E-MTAB-49181491395130:nuclear cycle 14 triptolide injected ChIP input repl 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: S-phase

text: fruit fly

text: nuclear cycle 14

text: wild type

text: w[*]; P{EGFP-PCNA}attP2

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed


name: E-MTAB-49181491395130:nuclear cycle 14 triptolide injected ChIP Pol II pan repl 1

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: S-phase

text: fruit fly

characteristic: common name

text: nuclear cycle 14

text: wild type

text: w[*]; P{EGFP-PCNA}attP2

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed


name: E-MTAB-49181491395130:nuclear cycle 14 triptolide injected ChIP Pol II pan repl 2

text: public

text: ArrayExpress

text: S-phase

text: fruit fly

characteristic: description

text: nuclear cycle 14

text: wild type

text: w[*]; P{EGFP-PCNA}attP2

characteristic: genotype

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

characteristic: title


name: E-MTAB-49181491395130:nuclear cycle 14 triptolide injected ChIP Pol II ser5p repl 1

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: S-phase

characteristic: cell cycle phase

text: fruit fly

text: nuclear cycle 14

characteristic: developmental stage

text: wild type

text: w[*]; P{EGFP-PCNA}attP2

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed


name: E-MTAB-49181491395130:nuclear cycle 14 triptolide injected ChIP Pol II ser5p repl 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: S-phase

text: fruit fly

text: nuclear cycle 14

text: wild type

characteristic: genetic modification

text: w[*]; P{EGFP-PCNA}attP2

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

characteristic: sex


name: E-MTAB-49181491395130:nuclear cycle 14 triptolide injected repl 1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: S-phase

text: fruit fly

text: nuclear cycle 14

text: wild type

text: w[*]; P{EGFP-PCNA}attP2

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed


name: E-MTAB-49181491395130:nuclear cycle 14 triptolide injected repl 2

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: S-phase

text: fruit fly

characteristic: common name

text: nuclear cycle 14

text: wild type

text: w[*]; P{EGFP-PCNA}attP2

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed


name: E-MTAB-49181491395130:nuclear cycle 14 triptolide injected repl 3

text: public

text: ArrayExpress

text: S-phase

text: fruit fly

characteristic: description

text: nuclear cycle 14

text: wild type

text: w[*]; P{EGFP-PCNA}attP2

characteristic: genotype

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

characteristic: title


E-MTAB-4363_2:Sample 1

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-4363_2:Sample 1

tag: Namespace:Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery University of Salerno

text: ArrayExpress

characteristic: cell line

text: human

text: Protocols: Stable clones expressing ERβ tagged with TAP-tag at either C-term (Ct -ERβ) or N-term (Nt-ERβ) were obtained from human breast cancer MCF-7 cells (ER-alpha positive; ATCC, Cat No. HTB-22) .Concerning the generation of ERβ tagged inducible clones, the human full-length cDNA clone pCMV6-ESR2 (RC218519) encoding human ESR2 was purchased from Origene (Rockville, MD). ESR2 sequence, including the Myc and Flag Tags, was then subcloned into the BamHI and EcoRI sites of the pTRE-Tight expression vector (Clontech, Mountain View, CA). All cell lines were propagated in Dulbecco’s modified Eagle medium (DMEM; Sigma-Aldrich) supplemented with 10% FBS (HyClone) and antibiotics: 100U/ml penicillin, 100mg/ml streptomycin, 250ng/ml Amfotericin-B. Steroid deprivation (starvation) was performed by culturing in DMEM w/o phenol red and 5% Dextran Coated Charcoal stripped serum (DCC-FBS) for 5 days. Cell lines were authenticated by short tandem repeat (STR) profiling and routinely tested for Mycoplasma contamination with MycoAlert mycoplasma detection kit (Lonza). Total RNA was extracted from cells expressing or not ERβ using the standard RNA extraction method with TRIzol (Life Technologies). Before use, RNA concentration in each sample was assayed with a ND-2000c spectrophotometer (Thermoscientific) and its quality and integrity assessed with the Agilent 2100 Bioanalyzer with Agilent RNA 6000 nano kit (Agilent Technologies). For RNA sequencing experiments, indexed libraries were prepared using 1 µg of total RNA as starting material, with TruSeq Stranded Total RNA Sample Prep Kit (Illumina Inc.). Libraries were sequenced (paired-end, 2x100 cycles) at a concentration of 8 pM/lane on HiSeq 2500 platform (Illumina Inc.)

text: breast carcinoma

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 1

type: has member


E-MTAB-4363_2:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery University of Salerno

text: public

text: E-MTAB-4363_2:Sample 2

text: ArrayExpress

text: human

text: breast carcinoma

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 2


E-MTAB-4363_2:Sample 3

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-4363_2:Sample 3

text: ArrayExpress

text: human

text: breast carcinoma

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 3


E-MTAB-4363_2:Sample 4

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-4363_2:Sample 4

text: ArrayExpress

text: human

text: breast carcinoma

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 4


E-MTAB-4363_2:Sample 5

text: public

characteristic: SRA accession

text: E-MTAB-4363_2:Sample 5

characteristic: Submitter Id

text: ArrayExpress

text: human

text: breast carcinoma

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 5


E-MTAB-4363_2:Sample 6

text: public

text: E-MTAB-4363_2:Sample 6

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: breast carcinoma

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 6


E-MTAB-4363_2:Sample 7

text: public

text: E-MTAB-4363_2:Sample 7

text: ArrayExpress

text: human

characteristic: description

text: breast carcinoma

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 7


E-MTAB-4363_2:Sample 8

text: public

text: E-MTAB-4363_2:Sample 8

text: ArrayExpress

text: human

text: breast carcinoma

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: Sample 8


E-MTAB-4363_2:Sample 9

text: public

text: E-MTAB-4363_2:Sample 9

text: ArrayExpress

text: human

text: breast carcinoma

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 9

characteristic: title


text: UOM

characteristic: INSDC center name

text: public

text: human

text: Egyptian mummy from Manchester Museum KNIII, Male

text: Homo sapiens

text: Homo sapiens

text: KNIII


text: UOM

characteristic: INSDC first public

text: public

text: human

text: Egyptian mummy from Manchester Museum NAII, Male

text: Homo sapiens

text: Homo sapiens

text: NAII


E-MTAB-5622:ETN treatment_Donor 1

text: public

text: E-MTAB-5622:ETN treatment_Donor 1

tag: Namespace:Radboud University Medical Center (Radboudumc)

text: ArrayExpress

text: CD4-positive, alpha-beta memory T cell

characteristic: cell type

text: human

text: Protocols: CD4+ T cells derived from healthy volunteers were isolated using Rosette Sep CD4+ enrichment cocktail (CAT#15022, StemCell® Technologies) (50 μL/ml of whole blood) according to the instructions of the supplier. To sort CD4+CD25-CD45RA- (Tmem) the purified CD4+ cells were washed and surface stained with anti-CD25-BV510® (M-A251, BD), anti-CD45RA- PE®(4KB5, Dako) and CD4-PE-Cy5.5® (13B8.2, Beckman-Coulter) and FACS-sorted on a FACSAria™ III machine (BD). FACS-sorted CD4+ Tmem cells (2.5 x 104 cells/well) were cultured in 96-well U-bottom plates and incubated with Dynabeads® Human T-Activator CD3/CD28 (1:5, bead:cell ratio) (Cat# 111.31D, Gibco®) and recombinant human IL-2 (rhIL-2) (100 U/mL) (Proleukin Prometheus Laboratories) for three days at 37C with 5% CO2. RPMI-1640 Dutch modified (Gibco®) culture medium, with sodium bicarbonate and 20 mM HEPES, supplemented with penicillin/streptomycin (100 U/mL), sodium pyruvate (1 mM), glutamine/glutamax and 10% human pooled serum (HPS, Radboudumc), was used in all conditions.] FACS-sorted CD4+ Tmem cultured as described in Protocol 2 (Growth protocol) were supplemented with TNF inhibitor (etanercept, Enbrel®, 5 µg/mL, Pfizer). On day three of culture the cells were pooled and RNA extraction was carried out. Total RNA was extracted from lysed CD4+ Tmem by using the RNeasy Plus Micro kit (Qiagen). Initial quality check and RNA quantification of the samples were performed by capillary electrophoresis using the LabChip GX (Perkin Elmer). Non-degraded RNA-samples were selected for subsequent sequencing analysis. Sequence libraries were generated using the TruSeq (polyA) mRNA sample preparation kits (Illumina) using the Sciclone NGS Liquid Handler (Perkin Elmer).

text: normal

text: anti-CD3/CD28-coated bead (1:5, bead:cell ratio) stimulation + recombinant human IL-2 (100 U/mL)

characteristic: growth condition

text: Donor 1

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: CD4+ CD25- CD45RA-

characteristic: phenotype

text: Homo sapiens

text: ETN treatment_Donor 1


E-MTAB-5622:ETN treatment_Donor 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Radboud University Medical Center (Radboudumc)

text: public

text: E-MTAB-5622:ETN treatment_Donor 2

text: ArrayExpress

text: CD4-positive, alpha-beta memory T cell

text: human

text: normal

characteristic: disease

text: Donor 2

text: Homo sapiens

text: Homo sapiens

text: blood

text: CD4+ CD25- CD45RA-

text: Homo sapiens

text: ETN treatment_Donor 2


E-MTAB-5622:ETN treatment_Donor 3

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5622:ETN treatment_Donor 3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: CD4-positive, alpha-beta memory T cell

text: human

text: normal

text: Donor 3

text: Homo sapiens

text: Homo sapiens

text: blood

text: CD4+ CD25- CD45RA-

text: Homo sapiens

text: ETN treatment_Donor 3


E-MTAB-5622:ETN treatment_Donor 4

characteristic: INSDC center name

text: public

text: E-MTAB-5622:ETN treatment_Donor 4

text: ArrayExpress

text: CD4-positive, alpha-beta memory T cell

text: human

characteristic: common name

characteristic: description

text: normal

text: Donor 4

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: CD4+ CD25- CD45RA-

text: Homo sapiens

text: ETN treatment_Donor 4

characteristic: title


characteristic: INSDC first public

text: public

text: E-MTAB-5622:rhTNF_alpha treatment_Donor 1

text: ArrayExpress

text: CD4-positive, alpha-beta memory T cell

characteristic: cell type

text: human

text: Protocols: CD4+ T cells derived from healthy volunteers were isolated using Rosette Sep CD4+ enrichment cocktail (CAT#15022, StemCell® Technologies) (50 μL/ml of whole blood) according to the instructions of the supplier. To sort CD4+CD25-CD45RA- (Tmem) the purified CD4+ cells were washed and surface stained with anti-CD25-BV510® (M-A251, BD), anti-CD45RA- PE®(4KB5, Dako) and CD4-PE-Cy5.5® (13B8.2, Beckman-Coulter) and FACS-sorted on a FACSAria™ III machine (BD). FACS-sorted CD4+ Tmem cells (2.5 x 104 cells/well) were cultured in 96-well U-bottom plates and incubated with Dynabeads® Human T-Activator CD3/CD28 (1:5, bead:cell ratio) (Cat# 111.31D, Gibco®) and recombinant human IL-2 (rhIL-2) (100 U/mL) (Proleukin Prometheus Laboratories) for three days at 37C with 5% CO2. RPMI-1640 Dutch modified (Gibco®) culture medium, with sodium bicarbonate and 20 mM HEPES, supplemented with penicillin/streptomycin (100 U/mL), sodium pyruvate (1 mM), glutamine/glutamax and 10% human pooled serum (HPS, Radboudumc), was used in all conditions.] FACS-sorted CD4+ Tmem cultured as described in Protocol 2 (Growth protocol) were supplemented with recombinant human TNF-alpha (rhTNF-alpha, 50 ng/mL, CAT# 210-TA-020, R&D). On day three of culture the cells were pooled and RNA extraction was carried out. Total RNA was extracted from lysed CD4+ Tmem by using the RNeasy Plus Micro kit (Qiagen). Initial quality check and RNA quantification of the samples were performed by capillary electrophoresis using the LabChip GX (Perkin Elmer). Non-degraded RNA-samples were selected for subsequent sequencing analysis. Sequence libraries were generated using the TruSeq (polyA) mRNA sample preparation kits (Illumina) using the Sciclone NGS Liquid Handler (Perkin Elmer).

text: normal

characteristic: growth condition

text: Donor 1

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: CD4+ CD25- CD45RA-

text: Homo sapiens

text: rhTNF_alpha treatment_Donor 1


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-5622:rhTNF_alpha treatment_Donor 3

text: ArrayExpress

text: CD4-positive, alpha-beta memory T cell

text: human

text: normal

text: Donor 2

text: Homo sapiens

text: Homo sapiens

text: blood

text: CD4+ CD25- CD45RA-

characteristic: phenotype

text: Homo sapiens

text: rhTNF_alpha treatment_Donor 3


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5622:rhTNF_alpha treatment_Donor 4

characteristic: Submitter Id

text: ArrayExpress

text: CD4-positive, alpha-beta memory T cell

text: human

text: normal

characteristic: disease

text: Donor 3

text: Homo sapiens

text: Homo sapiens

text: blood

text: CD4+ CD25- CD45RA-

text: Homo sapiens

text: rhTNF_alpha treatment_Donor 4


characteristic: INSDC center name

text: public

text: E-MTAB-5622:rhTNF_alpha treatment_Donor 5

text: ArrayExpress

characteristic: broker name

text: CD4-positive, alpha-beta memory T cell

text: human

characteristic: common name

characteristic: description

text: normal

text: Donor 4

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: CD4+ CD25- CD45RA-

text: Homo sapiens

text: rhTNF_alpha treatment_Donor 5


text: Bayer Pharma Aktiengesellschaft

characteristic: INSDC first public

text: public

text: E-MTAB-5209:01_151-ML-M-MF_VITRO_ALDH-NEG_ACAGTG

text: ArrayExpress

text: human

text: Protocols: 3D in vitro models of patient derived colon cancer tumors were processed to single cells, labelled for ALDH activity using the Aldefluor Assay and separated in ALDH- ad ALDH+ cell fractions Cells were lysed in RLTplus buffer and RNA was extracted using Qiagen RNeasy Mini Kit. RNA quality was assessed prior to sequencing TruSeq RNA V2 library construction protocol from Illumina

text: colon cancer

text: aldehyde dehydrogenase negative

characteristic: fraction

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Bayer Pharma Aktiengesellschaft

text: public

text: E-MTAB-5209:02_151-ML-M-MF_VITRO_ALDH-NEG_CAGATC

text: ArrayExpress

text: human

text: colon cancer

text: aldehyde dehydrogenase negative

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Bayer Pharma Aktiengesellschaft

text: public

text: E-MTAB-5209:05_162-MW-P-TF_VITRO_ALDH-NEG_CCGTCC

text: ArrayExpress

text: human

text: colon cancer

text: aldehyde dehydrogenase negative

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Bayer Pharma Aktiengesellschaft

characteristic: INSDC last update

text: public

text: E-MTAB-5209:06_162-MW-P-TF_VITRO_ALDH-NEG_GATCAG

text: ArrayExpress

text: human

text: colon cancer

text: aldehyde dehydrogenase negative

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Bayer Pharma Aktiengesellschaft

text: public

characteristic: INSDC status

text: E-MTAB-5209:09_195-CB-P-TF_VITRO_ALDH-NEG_ACTGAT

text: ArrayExpress

text: human

text: colon cancer

text: aldehyde dehydrogenase negative

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Bayer Pharma Aktiengesellschaft

text: public

characteristic: SRA accession

text: E-MTAB-5209:10_195-CB-P-TF_VITRO_ALDH-NEG_GGCTAC

text: ArrayExpress

text: human

text: colon cancer

text: aldehyde dehydrogenase negative

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Bayer Pharma Aktiengesellschaft

text: public

text: E-MTAB-5209:17_278-ML-P-TF_VITRO_ALDH-NEG_ATTCCT

characteristic: Submitter Id

text: ArrayExpress

text: human

text: colon cancer

text: aldehyde dehydrogenase negative

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Bayer Pharma Aktiengesellschaft

text: public

text: E-MTAB-5209:18_278-ML-P-TF_VITRO_ALDH-NEG_AGTTCC

text: ArrayExpress

text: human

text: colon cancer

characteristic: disease

text: aldehyde dehydrogenase negative

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Bayer Pharma Aktiengesellschaft

characteristic: INSDC center name

text: public

text: E-MTAB-5209:21_302-CB-M-MF_VITRO_ALDH-NEG_TAGCTT

text: ArrayExpress

text: human

text: colon cancer

text: aldehyde dehydrogenase negative

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Bayer Pharma Aktiengesellschaft

text: public

text: E-MTAB-5209:22_302-CB-M-MF_VITRO_ALDH-NEG_TAGCTT

text: ArrayExpress

characteristic: broker name

text: human

text: colon cancer

text: aldehyde dehydrogenase negative

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Bayer Pharma Aktiengesellschaft

text: public

text: E-MTAB-5209:25_151-ML-M-MF_VITRO_ALDH-POS_AGTCAA

text: ArrayExpress

text: human

characteristic: common name

text: colon cancer

text: aldehyde dehydrogenase positive

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Bayer Pharma Aktiengesellschaft

text: public

text: E-MTAB-5209:26_151-ML-M-MF_VITRO_ALDH-POS_TTAGGC

text: ArrayExpress

text: human

characteristic: description

text: colon cancer

text: aldehyde dehydrogenase positive

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Bayer Pharma Aktiengesellschaft

text: public

text: E-MTAB-5209:29_162-MW-P-TF_VITRO_ALDH-POS_ATTCCT

text: ArrayExpress

text: human

text: colon cancer

text: aldehyde dehydrogenase positive

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens


text: Bayer Pharma Aktiengesellschaft

characteristic: INSDC first public

text: public

text: E-MTAB-5209:30_162-MW-P-TF_VITRO_ALDH-POS_GTGAAA

text: ArrayExpress

text: human

text: colon cancer

text: aldehyde dehydrogenase positive

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Bayer Pharma Aktiengesellschaft

text: public

text: E-MTAB-5209:33_195-CB-P-TF_VITRO_ALDH-POS_GCCAAT

text: ArrayExpress

text: human

text: colon cancer

text: aldehyde dehydrogenase positive

characteristic: fraction

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Bayer Pharma Aktiengesellschaft

text: public

text: E-MTAB-5209:34_195-CB-P-TF_VITRO_ALDH-POS_GAGTGG

text: ArrayExpress

text: human

text: colon cancer

text: aldehyde dehydrogenase positive

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

text: Bayer Pharma Aktiengesellschaft

text: public

text: E-MTAB-5209:41_278-ML-P-TF_VITRO_ALDH-POS_TTAGGC

text: ArrayExpress

text: human

text: colon cancer

text: aldehyde dehydrogenase positive

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: Bayer Pharma Aktiengesellschaft

text: public

text: E-MTAB-5209:42_278-ML-P-TF_VITRO_ALDH-POS_ACTTGA

text: ArrayExpress

text: human

text: Protocols: 3D in vitro models of patient derived colon cancer tumors were processed to single cells, labelled for ALDH activity using the Aldefluor Assay and separated in ALDH- ad ALDH+ cell fractions Cells were lysed in RLTplus buffer and RNA was extracted using Qiagen RNeasy Mini Kit. RNA quality was assessed prior to sequencing TruSeq RNA V2 library construction protocol from Illumina

text: colon cancer

text: aldehyde dehydrogenase positive

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

text: Bayer Pharma Aktiengesellschaft

text: public

text: E-MTAB-5209:45_302-CB-M-MF_VITRO_ALDH-POS_CTTGTA

text: ArrayExpress

text: human

text: colon cancer

text: aldehyde dehydrogenase positive

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: External Id

text: Bayer Pharma Aktiengesellschaft

text: public

text: E-MTAB-5209:46_302-CB-M-MF_VITRO_ALDH-POS_CCGTCC

text: ArrayExpress

text: human

text: colon cancer

text: aldehyde dehydrogenase positive

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Bayer Pharma Aktiengesellschaft

characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

text: colon cancer

text: unfractionated

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Haematopoietic Stem Cell Clones

characteristic: ArrayExpress-PHENOTYPE

text: Mus musculus

characteristic: ArrayExpress-SPECIES

text: SC

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: Haematopoietic Stem Cell Clones

characteristic: phenotype

text: Mus musculus

characteristic: subject id


text: University of Lille 1

characteristic: INSDC center name

text: public

characteristic: SRA accession

tag: Namespace:University of Lille 1

characteristic: Submitter Id

characteristic: collection date

text: flax

text: Plant sample during flax retting, time point 1 corresponding to uprooting flax, plot ‘early’

text: agricultural site

characteristic: environment (biome)

text: agricultural site

characteristic: environment (feature)

text: Flax plant

characteristic: environment (material)

text: France

characteristic: geographic location (country and/or sea)

text: 49.9990 N

unit: DD

characteristic: geographic location (latitude)

text: 1.6884 E

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Linum usitatissimum

text: plant-associated

characteristic: plant-associated environmental package

text: Dew-retting flax

characteristic: project name

text: Linum usitatissimum

text: Illumina MiSeq

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Lille 1

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: flax

characteristic: common name

text: Plant sample during flax retting, time point 2, plot ‘early’

characteristic: description

text: agricultural site

text: agricultural site

text: Flax plant

text: France

text: 49.9990 N

text: 1.6884 E

text: metagenome

text: Linum usitatissimum

characteristic: organism

text: plant-associated

text: Dew-retting flax

text: Linum usitatissimum

text: Illumina MiSeq

characteristic: title


text: University of Lille 1

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: flax

text: Plant sample during flax retting, time point 3, plot ‘early’

text: agricultural site

characteristic: environment (biome)

text: agricultural site

characteristic: environment (feature)

text: Flax plant

characteristic: environment (material)

text: France

characteristic: geographic location (country and/or sea)

text: 49.9990 N

characteristic: geographic location (latitude)

text: 1.6884 E

text: metagenome

text: Linum usitatissimum

text: plant-associated

text: Dew-retting flax

text: Linum usitatissimum

text: Illumina MiSeq


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Lille 1

text: public

text: flax

text: Plant sample during flax retting, time point 4, plot ‘early’

text: agricultural site

text: agricultural site

text: Flax plant

text: France

text: 49.9990 N

text: 1.6884 E

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Linum usitatissimum

text: plant-associated

characteristic: plant-associated environmental package

text: Dew-retting flax

characteristic: project name

text: Linum usitatissimum

text: Illumina MiSeq

characteristic: sequencing method


text: University of Lille 1

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: flax

characteristic: common name

text: Plant sample during flax retting, time point 5, plot ‘early’

characteristic: description

text: agricultural site

text: agricultural site

text: Flax plant

text: France

text: 49.9990 N

text: 1.6884 E

text: metagenome

text: Linum usitatissimum

characteristic: organism

text: plant-associated

text: Dew-retting flax

text: Linum usitatissimum

text: Illumina MiSeq

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University of Lille 1

text: public

characteristic: Submitter Id

characteristic: collection date

text: flax

text: Plant sample during flax retting, time point 6, plot ‘early’

text: agricultural site

characteristic: environment (biome)

text: agricultural site

characteristic: environment (feature)

text: Flax plant

characteristic: environment (material)

text: France

characteristic: geographic location (country and/or sea)

text: 49.9990 N

characteristic: geographic location (latitude)

text: 1.6884 E

text: metagenome

text: Linum usitatissimum

text: plant-associated

text: Dew-retting flax

text: Linum usitatissimum

text: Illumina MiSeq


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Lille 1

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: flax

text: Plant sample during flax retting, time point 7, plot ‘early’

text: agricultural site

text: agricultural site

text: Flax plant

text: France

text: 49.9990 N

text: 1.6884 E

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Linum usitatissimum

text: plant-associated

characteristic: plant-associated environmental package

text: Dew-retting flax

characteristic: project name

text: Linum usitatissimum

text: Illumina MiSeq

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University of Lille 1

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: flax

characteristic: common name

text: Plant sample during flax retting, time point 1 corresponding to uprooting flax, plot ‘standard’

characteristic: description

text: agricultural site

text: agricultural site

text: Flax plant

text: France

text: 49.9990 N

text: 1.6884 E

text: metagenome

text: Linum usitatissimum

characteristic: organism

text: plant-associated

text: Dew-retting flax

text: Linum usitatissimum

text: Illumina MiSeq

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Lille 1

text: public

characteristic: Submitter Id

characteristic: collection date

text: flax

text: Plant sample during flax retting, time point 2, plot ‘standard’

text: agricultural site

characteristic: environment (biome)

text: agricultural site

characteristic: environment (feature)

text: Flax plant

characteristic: environment (material)

text: France

characteristic: geographic location (country and/or sea)

text: 49.9990 N

characteristic: geographic location (latitude)

text: 1.6884 E

text: metagenome

text: Linum usitatissimum

text: plant-associated

text: Dew-retting flax

text: Linum usitatissimum

text: Illumina MiSeq


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University of Lille 1

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: flax

text: Plant sample during flax retting, time point 3, plot ‘standard’

text: agricultural site

text: agricultural site

text: Flax plant

text: France

text: 49.9990 N

text: 1.6884 E

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Linum usitatissimum

text: plant-associated

characteristic: plant-associated environmental package

text: Dew-retting flax

characteristic: project name

text: Linum usitatissimum

text: Illumina MiSeq

characteristic: sequencing method


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Lille 1

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: flax

characteristic: common name

text: Plant sample during flax retting, time point 4, plot ‘standard’

characteristic: description

text: agricultural site

text: agricultural site

text: Flax plant

text: France

text: 49.9990 N

text: 1.6884 E

text: metagenome

text: Linum usitatissimum

characteristic: organism

text: plant-associated

text: Dew-retting flax

text: Linum usitatissimum

text: Illumina MiSeq

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University of Lille 1

text: public

characteristic: Submitter Id

characteristic: collection date

text: flax

text: Plant sample during flax retting, time point 5, plot ‘standard’

text: agricultural site

characteristic: environment (biome)

text: agricultural site

characteristic: environment (feature)

text: Flax plant

characteristic: environment (material)

text: France

characteristic: geographic location (country and/or sea)

text: 49.9990 N

characteristic: geographic location (latitude)

text: 1.6884 E

text: metagenome

text: Linum usitatissimum

text: plant-associated

text: Dew-retting flax

text: Linum usitatissimum

text: Illumina MiSeq


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Lille 1

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: flax

text: Plant sample during flax retting, time point 6, plot ‘standard’

text: agricultural site

text: agricultural site

text: Flax plant

text: France

text: 49.9990 N

text: 1.6884 E

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Linum usitatissimum

text: plant-associated

characteristic: plant-associated environmental package

text: Dew-retting flax

characteristic: project name

text: Linum usitatissimum

text: Illumina MiSeq

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University of Lille 1

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: flax

characteristic: common name

text: Plant sample during flax retting, time point 7, plot ‘standard’

characteristic: description

text: agricultural site

text: agricultural site

text: Flax plant

text: France

text: 49.9990 N

text: 1.6884 E

text: metagenome

text: Linum usitatissimum

characteristic: organism

text: plant-associated

text: Dew-retting flax

text: Linum usitatissimum

text: Illumina MiSeq

characteristic: title


EDCC 5458

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: JUSTUS LIEBIG UNIVERSITAT

text: public

text: EDCC 5458

tag: Namespace:JUSTUS LIEBIG UNIVERSITAT

characteristic: Submitter Id

characteristic: collection date

text: Here, we report the high-quality complete genome sequence of Staphylococcus aureus subsp. aureus EDCC 5458. Whole genome sequencing of this clinical strain revealed the complete genome sequence with 2,848,525 bp.

text: Germany

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: Clinical isolate

characteristic: isolate

text: Implant-associated infection

characteristic: isolation source

text: Staphylococcus aureus subsp. aureus

text: Staphylococcus aureus subsp. aureus

text: Complete genome sequence of Staphylococcus aureus subsp. aureus EDCC 5458 isolated from implant associated bone infections


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human-associated habitat [ENVO:00009003]

characteristic: environment (biome)

text: intestine environment [ENVO:2100002]

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: human-gut

characteristic: environment package

text: Germany

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: parkinson

characteristic: host disease status

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: human gut metagenome

text: The fecal microbiota in L-DOPA naive PD patients

characteristic: project name

text: human gut metagenome

text: Illumina

characteristic: sequencing method

text: stool sample


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: intestine environment [ENVO:2100002]

text: feces

text: human-gut

text: Germany

characteristic: geographic location (country and/or sea)

text: control

text: human-gut

text: metagenome

text: human gut metagenome

characteristic: organism

text: human gut metagenome

text: Illumina

text: stool sample

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:Genomic Big Data Center, Asia University

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: Gene expression profiling of TCMADR


text: Genomic Big Data Center, Asia University

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Gene expression profiling of TCMADR


EDCC 5464

text: JUSTUS LIEBIG UNIVERSITAT

text: public

text: EDCC 5464

text: Staphylococcus aureus subsp. aureus EDCC 5464

characteristic: description

text: Germany

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: clinical isolate

characteristic: isolate

text: Implant-associated bone infections

characteristic: isolation source

text: Staphylococcus aureus subsp. aureus

text: Staphylococcus aureus subsp. aureus


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: URMITE

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: sputum

text: Mycobacterium sp. AFP003

text: Mycobacterium sp. AFP003

characteristic: strain

text: Mycobacterium ahvazicum


text: ANAND

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Terrestrial

characteristic: environment (biome)

text: Research Station

characteristic: environment (feature)

text: Organic Material

characteristic: environment (material)

text: India

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Cecum

characteristic: host body site

text: Chicken

characteristic: host common name

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: metagenome

characteristic: organism

text: Host Transcriptomics and gut microbiome analysis in broilers with contrasting Feed Conversion Ratio

characteristic: project name

text: metagenome

text: illumina

characteristic: sequencing method

text: Chicken Cecal Microbiome


E-MTAB-5641:Sample 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5641:Sample 1

tag: Namespace:Sainsbury Laboratory, University of Cambridge

unit: day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: thale cress

characteristic: common name

text: Protocols: A. thaliana seeds were surfaced sterilized and sown in petri dishes with agarified (0.8% Bacto Agar, Becton Dickinson) 0.5x MS medium (Duchefa), containing 1% sucrose and 0.05% MES at pH 5.7. After 3 days of stratification at 4°C, plants were grown in a CU-22L growth chamber (Percival) under 12/12 hours (day/night) light cycle. For the heat-induction, 7 days old plants grown at 21°C were first placed for 24 hours on top of a chilling platform build-in within the growth chamber and maintained by an external mini-chiller at 4°C, but with the chamber temperature set at 6°C. This was followed by 24 hours with the chamber set at 37°C for the stressed plants, whereas control plants were moved back to 21°C. DNeasy Plant Mini Kit (Quiagen). PCR-free libraries for genome sequencing were prepared with 1 µg of DNA using the TruSeq DNA PCR-Free Library Prep kit (Illumina); following provider’s instructions.

characteristic: description

text: seedling

characteristic: developmental stage

characteristic: ecotype

text: wild type

characteristic: genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: whole organism

characteristic: organism part

text: Arabidopsis thaliana

text: Sample 1

characteristic: title


E-MTAB-5641:Sample 3

characteristic: ENA-CHECKLIST

text: Sainsbury Laboratory, University of Cambridge

text: public

characteristic: SRA accession

text: E-MTAB-5641:Sample 3

characteristic: Submitter Id

text: ArrayExpress

text: thale cress

text: seedling

text: nrpd1-3 mutant

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: whole organism

text: Arabidopsis thaliana

text: Sample 3


E-MTAB-5641:Sample 2

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-5641:Sample 2

text: ArrayExpress

text: thale cress

text: seedling

text: wild type

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: whole organism

text: Arabidopsis thaliana

text: Sample 2


E-MTAB-5641:Sample 4

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5641:Sample 4

characteristic: age

text: ArrayExpress

text: thale cress

text: seedling

text: nrpd1-3 mutant

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: whole organism

text: Arabidopsis thaliana

text: Sample 4


E-MTAB-5643:Sample 5

text: public

text: E-MTAB-5643:Sample 5

text: ArrayExpress

characteristic: broker name

text: thale cress

characteristic: common name

text: Protocols: A. thaliana seeds were surfaced sterilized and sown in petri dishes with agarified (0.8% Bacto Agar, Becton Dickinson) 0.5x MS medium (Duchefa), containing 1% sucrose and 0.05% MES at pH 5.7. After 3 days of stratification at 4°C, plants were grown in a CU-22L growth chamber (Percival) under 12/12 hours (day/night) light cycle. For the heat-induction, 7 days old plants grown at 21°C were first placed for 24 hours on top of a chilling platform build-in within the growth chamber and maintained by an external mini-chiller at 4°C, but with the chamber temperature set at 6°C. This was followed by 24 hours with the chamber set at 37°C for the stressed plants, whereas control plants were moved back to 21°C. RNA was isolated using the Plant-RNAeasy kit (Invitrogen). Strand-specific libraries for RNA-seq were prepared with 2 µg of RNA using the TruSeq Stranded Total RNA Library Prep Kit (Illumina); following the provider’s instructions.

characteristic: description

text: seedling

characteristic: developmental stage

text: nrpd1-3 mutant

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: whole organism

text: Arabidopsis thaliana

text: Sample 5


E-MTAB-5643:Sample 6

text: public

text: E-MTAB-5643:Sample 6

text: ArrayExpress

text: thale cress

text: seedling

characteristic: ecotype

text: nrpd1-3 mutant

characteristic: genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: whole organism

characteristic: organism part

text: Arabidopsis thaliana

text: Sample 6

characteristic: title


E-MTAB-5643:Sample 7

characteristic: ENA-CHECKLIST

text: public

characteristic: SRA accession

text: E-MTAB-5643:Sample 7

characteristic: Submitter Id

text: ArrayExpress

text: thale cress

text: seedling

text: nrpd1-3 mutant

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: whole organism

text: Arabidopsis thaliana

text: Sample 7


E-MTAB-5643:Sample 8

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-5643:Sample 8

text: ArrayExpress

text: thale cress

text: seedling

text: nrpd1-3 mutant

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: whole organism

text: Arabidopsis thaliana

text: Sample 8


E-MTAB-5643:Sample 1

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5643:Sample 1

characteristic: age

text: ArrayExpress

text: thale cress

text: seedling

text: wild type

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: whole organism

text: Arabidopsis thaliana

text: Sample 1


E-MTAB-5643:Sample 2

text: public

text: E-MTAB-5643:Sample 2

text: ArrayExpress

characteristic: broker name

text: thale cress

characteristic: common name

characteristic: description

text: seedling

characteristic: developmental stage

text: wild type

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: whole organism

text: Arabidopsis thaliana

text: Sample 2


E-MTAB-5643:Sample 3

text: public

text: E-MTAB-5643:Sample 3

text: ArrayExpress

text: thale cress

text: seedling

characteristic: ecotype

text: wild type

characteristic: genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: whole organism

characteristic: organism part

text: Arabidopsis thaliana

text: Sample 3

characteristic: title


E-MTAB-5643:Sample 4

characteristic: ENA-CHECKLIST

text: public

characteristic: SRA accession

text: E-MTAB-5643:Sample 4

characteristic: Submitter Id

text: ArrayExpress

text: thale cress

text: seedling

text: wild type

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: whole organism

text: Arabidopsis thaliana

text: Sample 4


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CBMSO

characteristic: INSDC center name

text: public

text: In this project, we have sequenced again the genome of this strain by the use of two NGS technologies: Illumina sequencing and single-molecule, real-time sequencing (Pacific Biosciences, PacBio).

text: Leishmania infantum

text: Leishmania infantum

text: de novo assembly Leishmania infantum


text: RWTH Aachen

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:RWTH Aachen

text: Cuscuta campestris

text: Cuscuta campestris

text: Cuscuta campestris detached from host, 1d in water in the dark after Far red light induction of haustorial development - Biological replicate 1


text: RWTH Aachen

text: public

text: Cuscuta campestris

text: Cuscuta campestris

text: Cuscuta campestris detached from host, 1d in water in the dark after Far red light induction of haustorial development - Biological replicate 2


text: RWTH Aachen

text: public

text: Cuscuta campestris

text: Cuscuta campestris

text: Cuscuta campestris detached from host, 1d in water in the dark after Far red light induction of haustorial development - Biological replicate 3


text: RWTH Aachen

text: public

text: Cuscuta campestris

text: Cuscuta campestris

text: Cuscuta campestris detached from host, 3d in water in the dark - Biological replicate 1


text: RWTH Aachen

text: public

text: Cuscuta campestris

text: Cuscuta campestris

text: Cuscuta campestris detached from host, 3d in water in the dark - Biological replicate 2


text: RWTH Aachen

text: public

text: Cuscuta campestris

text: Cuscuta campestris

text: Cuscuta campestris detached from host, 3d in water in the dark - Biological replicate 3


text: RWTH Aachen

text: public

text: Cuscuta campestris

text: Cuscuta campestris

text: Cuscuta campestris on host - Biological replicate 1


text: RWTH Aachen

text: public

text: Cuscuta campestris

text: Cuscuta campestris

text: Cuscuta campestris on host - Biological replicate 2


text: RWTH Aachen

text: public

text: Cuscuta campestris

text: Cuscuta campestris

text: Cuscuta campestris on host - Biological replicate 3


text: RWTH Aachen

text: public

text: Cuscuta campestris

text: Cuscuta campestris

text: Cuscuta detached from host, 3d in water, Nutation around a wooden rod - Biological replicate 1


text: RWTH Aachen

text: public

text: Cuscuta campestris

text: Cuscuta campestris

text: Cuscuta detached from host, 3d in water, Nutation around a wooden rod - Biological replicate 2


text: RWTH Aachen

text: public

text: Cuscuta campestris

text: Cuscuta campestris

text: Cuscuta detached from host, 3d in water, Nutation around a wooden rod - Biological replicate 3


text: RWTH Aachen

text: public

text: Cuscuta campestris

text: Cuscuta campestris

text: Cuscuta detached from host, 3d in water - Biological replicate 1


text: RWTH Aachen

text: public

text: Cuscuta campestris

text: Cuscuta campestris

text: Cuscuta detached from host, 3d in water - Biological replicate 2


text: RWTH Aachen

text: public

text: Cuscuta campestris

text: Cuscuta campestris

text: Cuscuta detached from host, 3d in water - Biological replicate 3


text: UH

text: public

characteristic: collection date

text: beef day 11

characteristic: description

text: anthropogenic environmental material

characteristic: environment (biome)

text: agricultural environmental material

characteristic: environment (feature)

text: biological product

characteristic: environment (material)

text: Finland

characteristic: geographic location (country and/or sea)

text: 60.2251° N

characteristic: geographic location (latitude)

text: 25.0201° E

characteristic: geographic location (longitude)

text: metatranscriptome

characteristic: investigation type

text: miscellaneous natural or artificial environment

characteristic: miscellaneous environmental package

text: food metagenome

text: food spoilage

characteristic: project name

text: food metagenome

text: illumina

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CBMSO

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Leishmania infantum

characteristic: organism

text: Leishmania infantum

text: de novo assembly Leishmania infantum

characteristic: title


text: CBMSO

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Leishmania infantum

text: Leishmania infantum

text: de novo assembly of Leishmania infantum


text: ANAND

text: public

characteristic: collection date

text: Terrestrial

characteristic: environment (biome)

text: Research station

characteristic: environment (feature)

text: Organic material

characteristic: environment (material)

text: India

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Ileum

characteristic: host body site

text: Chicken

characteristic: host common name

text: host-associated

characteristic: host-associated environmental package

text: metagenome

text: metagenome

text: Host Transcriptomics and gut microbiome analysis in broilers with contrasting Feed Conversion Ratio

text: metagenome

text: Illumina

text: Chicken Ileum Microbiome


Blood

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INSTITUTE OF CANCER RESEARCH

text: public

characteristic: SRA accession

text: Blood

tag: Namespace:INSTITUTE OF CANCER RESEARCH

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens


text: ANAND

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: collection date

text: Terrestrial

text: Research station

text: Organic Material

text: India

text: host-associated

text: metagenome

characteristic: investigation type

text: metagenome

characteristic: organism

characteristic: project name

text: metagenome

text: Illumina

characteristic: sequencing method

text: Chicken Jejunum Microbiome

characteristic: title


characteristic: ENA-CHECKLIST

text: public

tag: Namespace:Department of Biochemistry and Molecular Biology, University of Southern Denmark

text: ArrayExpress

characteristic: broker name

text: Protocols: Plasmid transformed UTI89/pMWLib culture was grown at 37 °C for 1 hour without aeration in preheated DMEM with 10 % FBS containing 100 μg/mL ampicillin (amp) for plasmid selection. UTI89/pMWLib cells emitting green fluorescence were collected by cell sorting, using an FACSAria II. The bacteria were then collected by centrifugation at 3500xg for 10 minutes, resuspended in LB and grown overnight. The UTI89 promoter trap library was constructed as described by Bumann and Valdivia (Nat Protoc 2007, 2: 770-777) with minor modifications. Chromosomal DNA was purified from an overnight culture of UTI89. Bacterial cells were harvested and resuspended in TE buffer (0.089 % Trizma hydrochloride (w/v), 0.053 % Trizma base (w/v) and 0.1 mM EDTA), rapid lysis buffer (5 % sodium dodecyl sulfate (SDS), 0.125 M EDTA, 0.5 M Tris-HCl pH 9.4), Ribonuclease A (Sigma Aldrich) and protease (Roche) (37°C) and incubated for one hour at 37 °C. Chromosomal DNA was purified by phenol-chloroform extraction, precipitated by addition of 2 vol. 96% ethanol, and resuspended in TE-buffer. Purified genomic DNA (100ng/ml) was disrupted by sonication for 2x30 seconds using a Branson Sonifier 250 (Branson Ultrasonics). Resulting fragments of 500-700 bp were purified from a 2% agarose gel using a GFX PCR DNA and Gel Band purification kit (GE Healtcare) and treated with T4 polymerase (New England Biolabs) for 15 minutes at 12 °C to repair single-stranded regions. The library vector pMW82 was cleaved with BamHI (Fermentas) and SphI (Fermentas), and treated with T4 polymerase to fill in single-stranded overhangs. Next, treatment with shrimp alkaline phosphatase (USB Corporation) was included to prevent vector re-ligation. Finally, genomic fragments and vector DNA was ligated using T4 DNA ligase. Ligated DNA was introduced into MegaX DH10BTM T1R ElectrocompTM Cells (Invitrogen) by electroporation, and transformants were selected by plating on LB agar containing 100 μg/ml amp. The frequency of vector re-ligation was estimated to be less than 20 %. Plasmids were subsequently purified using NucleoBond AX kit (Macherey-Nagel) and transformed into E. coli UTI89 by electroporation. The resulting amp-resistant colonies, together constituting the promoter trap library UTI89/pMWLib, were pooled and frozen at -80°C. Plasmids were purified from sorted UTI89/pMWLib using NucleoBond PC 500 kit (Macherey-Nagel) as specified by the manufacturer. PCR amplification of the inserted chromosome segments in pMWLib was performed using primers P1 (5’-TGAAGGCTCTCAAGGGCATC-3’) and P2 (5’-GTGTTGGCCATGGAACAGGT-3’). DNA fragments were sonicated into 250-400 bp long segments from the original size of 500-700 bp, and sequencing library preparation was performed according to the manufacturer’s instructions (Illumina) as described previously (Nielsen R, Mandrup S. Methods Enzymol 2014, 537: 261-279).

characteristic: description

text: DMEM medium

characteristic: growth condition

text: J82 Bladder Epithelial Cells (BECs)

characteristic: host

text: Escherichia coli UTI89

text: Escherichia coli UTI89

text: Escherichia coli UTI89

text: Plasmid transformed UTI89/pMWLib

characteristic: strain

text: DMEM


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Biochemistry and Molecular Biology, University of Southern Denmark

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: Protocols: J82 Bladder Epithelial Cells (BECs) (ATCC® HTB-1™) were maintained at 5 % CO2, as a monolayer in DMEM (ThermoFisher Scientific) containing 10 % (v/v) heat-inactivated fetal bovine serum (FBS) (Gibco) and Penicillin (100 units/ml)-Streptomycin (100 μg/ml) (Gibco). The J82 BECs were grown to confluence in 15 cm dishes and subsequently infected with plasmid transformed UTI89/pMWLib at a multiplicity of infection of 10 for 1 hour at 37°C. The cells were then washed three times with PBS to remove non-invading bacteria and incubated in DMEM with 10 % FBS and 100 μg/ml gentamicin for 2 hours. Next, infected cells were washed three times with PBS to remove the gentamicin before 0.25 % trypsin-EDTA was added for 5 minutes to release the cells into suspension. The cells were collected by centrifugation at 150 xg and 4°C for 10 min and resuspended in PBS containing 10 % FBS. J82 cells emitting green fluorescence were collected by cell sorting, using an FACSAria II. In order to preserve the samples, cell sorting was performed for a maximum of 1 hour per sample, so several infection assays were set up to allow for successive sorting of multiple samples. Finally, bacteria were released from the J82 cells by addition of 1 % Triton X-100 and vortexing for 60 seconds. The bacteria were then collected by centrifugation at 3500xg for 10 minutes, resuspended in LB and grown overnight. The UTI89 promoter trap library was constructed as described by Bumann and Valdivia (Nat Protoc 2007, 2: 770-777) with minor modifications. Chromosomal DNA was purified from an overnight culture of UTI89. Bacterial cells were harvested and resuspended in TE buffer (0.089 % Trizma hydrochloride (w/v), 0.053 % Trizma base (w/v) and 0.1 mM EDTA), rapid lysis buffer (5 % sodium dodecyl sulfate (SDS), 0.125 M EDTA, 0.5 M Tris-HCl pH 9.4), Ribonuclease A (Sigma Aldrich) and protease (Roche) (37°C) and incubated for one hour at 37 °C. Chromosomal DNA was purified by phenol-chloroform extraction, precipitated by addition of 2 vol. 96% ethanol, and resuspended in TE-buffer. Purified genomic DNA (100ng/ml) was disrupted by sonication for 2x30 seconds using a Branson Sonifier 250 (Branson Ultrasonics). Resulting fragments of 500-700 bp were purified from a 2% agarose gel using a GFX PCR DNA and Gel Band purification kit (GE Healtcare) and treated with T4 polymerase (New England Biolabs) for 15 minutes at 12 °C to repair single-stranded regions. The library vector pMW82 was cleaved with BamHI (Fermentas) and SphI (Fermentas), and treated with T4 polymerase to fill in single-stranded overhangs. Next, treatment with shrimp alkaline phosphatase (USB Corporation) was included to prevent vector re-ligation. Finally, genomic fragments and vector DNA was ligated using T4 DNA ligase. Ligated DNA was introduced into MegaX DH10BTM T1R ElectrocompTM Cells (Invitrogen) by electroporation, and transformants were selected by plating on LB agar containing 100 μg/ml amp. The frequency of vector re-ligation was estimated to be less than 20 %. Plasmids were subsequently purified using NucleoBond AX kit (Macherey-Nagel) and transformed into E. coli UTI89 by electroporation. The resulting amp-resistant colonies, together constituting the promoter trap library UTI89/pMWLib, were pooled and frozen at -80°C. Plasmids were purified from sorted UTI89/pMWLib using NucleoBond PC 500 kit (Macherey-Nagel) as specified by the manufacturer. PCR amplification of the inserted chromosome segments in pMWLib was performed using primers P1 (5’-TGAAGGCTCTCAAGGGCATC-3’) and P2 (5’-GTGTTGGCCATGGAACAGGT-3’). DNA fragments were sonicated into 250-400 bp long segments from the original size of 500-700 bp, and sequencing library preparation was performed according to the manufacturer’s instructions (Illumina) as described previously (Nielsen R, Mandrup S. Methods Enzymol 2014, 537: 261-279).

text: J82 Bladder Epithelial Cells

text: J82 Bladder Epithelial Cells (BECs)

text: Escherichia coli UTI89

text: Escherichia coli UTI89

text: Escherichia coli UTI89

text: Plasmid transformed UTI89/pMWLib


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: Protocols: Plasmid transformed UTI89/pMWLib culture was grown to mid-exponential phase (4-5 generations) at 37°C with aeration in preheated LB medium with 100 μg/ml ampicillin. UTI89/pMWLib cells emitting green fluorescence were collected by cell sorting, using an FACSAria II. The bacteria were then collected by centrifugation at 3500xg for 10 minutes, resuspended in LB and grown overnight. The UTI89 promoter trap library was constructed as described by Bumann and Valdivia (Nat Protoc 2007, 2: 770-777) with minor modifications. Chromosomal DNA was purified from an overnight culture of UTI89. Bacterial cells were harvested and resuspended in TE buffer (0.089 % Trizma hydrochloride (w/v), 0.053 % Trizma base (w/v) and 0.1 mM EDTA), rapid lysis buffer (5 % sodium dodecyl sulfate (SDS), 0.125 M EDTA, 0.5 M Tris-HCl pH 9.4), Ribonuclease A (Sigma Aldrich) and protease (Roche) (37°C) and incubated for one hour at 37 °C. Chromosomal DNA was purified by phenol-chloroform extraction, precipitated by addition of 2 vol. 96% ethanol, and resuspended in TE-buffer. Purified genomic DNA (100ng/ml) was disrupted by sonication for 2x30 seconds using a Branson Sonifier 250 (Branson Ultrasonics). Resulting fragments of 500-700 bp were purified from a 2% agarose gel using a GFX PCR DNA and Gel Band purification kit (GE Healtcare) and treated with T4 polymerase (New England Biolabs) for 15 minutes at 12 °C to repair single-stranded regions. The library vector pMW82 was cleaved with BamHI (Fermentas) and SphI (Fermentas), and treated with T4 polymerase to fill in single-stranded overhangs. Next, treatment with shrimp alkaline phosphatase (USB Corporation) was included to prevent vector re-ligation. Finally, genomic fragments and vector DNA was ligated using T4 DNA ligase. Ligated DNA was introduced into MegaX DH10BTM T1R ElectrocompTM Cells (Invitrogen) by electroporation, and transformants were selected by plating on LB agar containing 100 μg/ml amp. The frequency of vector re-ligation was estimated to be less than 20 %. Plasmids were subsequently purified using NucleoBond AX kit (Macherey-Nagel) and transformed into E. coli UTI89 by electroporation. The resulting amp-resistant colonies, together constituting the promoter trap library UTI89/pMWLib, were pooled and frozen at -80°C. Plasmids were purified from sorted UTI89/pMWLib using NucleoBond PC 500 kit (Macherey-Nagel) as specified by the manufacturer. PCR amplification of the inserted chromosome segments in pMWLib was performed using primers P1 (5’-TGAAGGCTCTCAAGGGCATC-3’) and P2 (5’-GTGTTGGCCATGGAACAGGT-3’). DNA fragments were sonicated into 250-400 bp long segments from the original size of 500-700 bp, and sequencing library preparation was performed according to the manufacturer’s instructions (Illumina) as described previously (Nielsen R, Mandrup S. Methods Enzymol 2014, 537: 261-279).

text: LB medium

text: J82 Bladder Epithelial Cells (BECs)

text: Escherichia coli UTI89

text: Escherichia coli UTI89

text: Escherichia coli UTI89

text: Plasmid transformed UTI89/pMWLib

text: LB


text: public

text: ArrayExpress

text: Protocols: Plasmid transformed UTI89/pMWLib culture was grown to mid-exponential phase (4-5 generations) at 37°C with aeration in preheated human urine (USG 1.021) with 100 μg/ml ampicillin. UTI89/pMWLib cells emitting green fluorescence were collected by cell sorting, using an FACSAria II. The bacteria were then collected by centrifugation at 3500xg for 10 minutes, resuspended in LB and grown overnight. The UTI89 promoter trap library was constructed as described by Bumann and Valdivia (Nat Protoc 2007, 2: 770-777) with minor modifications. Chromosomal DNA was purified from an overnight culture of UTI89. Bacterial cells were harvested and resuspended in TE buffer (0.089 % Trizma hydrochloride (w/v), 0.053 % Trizma base (w/v) and 0.1 mM EDTA), rapid lysis buffer (5 % sodium dodecyl sulfate (SDS), 0.125 M EDTA, 0.5 M Tris-HCl pH 9.4), Ribonuclease A (Sigma Aldrich) and protease (Roche) (37°C) and incubated for one hour at 37 °C. Chromosomal DNA was purified by phenol-chloroform extraction, precipitated by addition of 2 vol. 96% ethanol, and resuspended in TE-buffer. Purified genomic DNA (100ng/ml) was disrupted by sonication for 2x30 seconds using a Branson Sonifier 250 (Branson Ultrasonics). Resulting fragments of 500-700 bp were purified from a 2% agarose gel using a GFX PCR DNA and Gel Band purification kit (GE Healtcare) and treated with T4 polymerase (New England Biolabs) for 15 minutes at 12 °C to repair single-stranded regions. The library vector pMW82 was cleaved with BamHI (Fermentas) and SphI (Fermentas), and treated with T4 polymerase to fill in single-stranded overhangs. Next, treatment with shrimp alkaline phosphatase (USB Corporation) was included to prevent vector re-ligation. Finally, genomic fragments and vector DNA was ligated using T4 DNA ligase. Ligated DNA was introduced into MegaX DH10BTM T1R ElectrocompTM Cells (Invitrogen) by electroporation, and transformants were selected by plating on LB agar containing 100 μg/ml amp. The frequency of vector re-ligation was estimated to be less than 20 %. Plasmids were subsequently purified using NucleoBond AX kit (Macherey-Nagel) and transformed into E. coli UTI89 by electroporation. The resulting amp-resistant colonies, together constituting the promoter trap library UTI89/pMWLib, were pooled and frozen at -80°C. Plasmids were purified from sorted UTI89/pMWLib using NucleoBond PC 500 kit (Macherey-Nagel) as specified by the manufacturer. PCR amplification of the inserted chromosome segments in pMWLib was performed using primers P1 (5’-TGAAGGCTCTCAAGGGCATC-3’) and P2 (5’-GTGTTGGCCATGGAACAGGT-3’). DNA fragments were sonicated into 250-400 bp long segments from the original size of 500-700 bp, and sequencing library preparation was performed according to the manufacturer’s instructions (Illumina) as described previously (Nielsen R, Mandrup S. Methods Enzymol 2014, 537: 261-279).

text: Urine

text: J82 Bladder Epithelial Cells (BECs)

text: Escherichia coli UTI89

characteristic: organism

text: Escherichia coli UTI89

text: Escherichia coli UTI89

text: Plasmid transformed UTI89/pMWLib

text: Urine


text: UTRECHT UNIVERSITY

text: public

tag: Namespace:UTRECHT UNIVERSITY

text: Escherichia coli

characteristic: common name

text: E. coli W3110 conjugant carrying plasmid p12S05199-3

text: Escherichia coli

text: Escherichia coli

characteristic: title


characteristic: ENA-CHECKLIST

text: UTRECHT UNIVERSITY

text: public

text: Escherichia coli

text: E. coli W3110 conjugant carrying plasmid p12S05199-4

text: Escherichia coli

text: Escherichia coli


text: UTRECHT UNIVERSITY

text: public

text: Escherichia coli

text: E. coli W3110 conjugant carrying plasmid p12S05205-1

characteristic: description

text: Escherichia coli

text: Escherichia coli


text: UTRECHT UNIVERSITY

text: public

text: Escherichia coli

text: E. coli W3110 conjugant carrying plasmid p12S05214-1

text: Escherichia coli

text: Escherichia coli


text: UTRECHT UNIVERSITY

text: public

text: Escherichia coli

text: E. coli W3110 conjugant carrying plasmid p12S05234-1

text: Escherichia coli

text: Escherichia coli


text: UTRECHT UNIVERSITY

text: public

text: Escherichia coli

text: E. coli W3110 conjugant carrying plasmid p12S05273-1

text: Escherichia coli

text: Escherichia coli


text: UTRECHT UNIVERSITY

text: public

text: Escherichia coli

text: E. coli W3110 conjugant carrying plasmid p12S05273-2

text: Escherichia coli

text: Escherichia coli


text: UTRECHT UNIVERSITY

text: public

text: Escherichia coli

text: E. coli W3110 conjugant carrying plasmid p12S05493-1

text: Escherichia coli

text: Escherichia coli


text: UTRECHT UNIVERSITY

text: public

text: Escherichia coli

text: E. coli W3110 conjugant carrying plasmid p12S05498-1

text: Escherichia coli

text: Escherichia coli


text: UTRECHT UNIVERSITY

text: public

text: Escherichia coli

text: E. coli W3110 conjugant carrying plasmid p12S05512-1

text: Escherichia coli

text: Escherichia coli


text: UTRECHT UNIVERSITY

text: public

text: Escherichia coli

text: E. coli W3110 conjugant carrying plasmid p12S05515-1

text: Escherichia coli

text: Escherichia coli


text: UTRECHT UNIVERSITY

text: public

text: Escherichia coli

text: E. coli W3110 conjugant carrying plasmid p12S05515-2

text: Escherichia coli

text: Escherichia coli


text: UTRECHT UNIVERSITY

text: public

text: Escherichia coli

text: E. coli W3110 conjugant carrying plasmid p5199

text: Escherichia coli

text: Escherichia coli


text: UTRECHT UNIVERSITY

text: public

text: Escherichia coli

text: E. coli W3110

text: Escherichia coli

text: Escherichia coli


text: VCU

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: human

text: Protocols: RNA was harvested from H1299 cells stably transfected with empty vector (Vector) or the p53 mutant (R273H). Total RNA was sent for sequencing. RNA was harvested from H1299 cells stably transfected with empty vector (Vector) or the p53 mutant (R273H). Total RNA was sent for sequencing.

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


E-MTAB-5652:pcmv Bam-1

characteristic: ENA-FIRST-PUBLIC

text: VCU

text: public

text: E-MTAB-5652:pcmv Bam-1

text: ArrayExpress

text: human

text: pcmv Bam

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: pcmv Bam-1


E-MTAB-5652:pcmv Bam-2

characteristic: ENA-LAST-UPDATE

text: VCU

text: public

text: E-MTAB-5652:pcmv Bam-2

text: ArrayExpress

text: human

text: pcmv Bam

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: pcmv Bam-2


E-MTAB-5653:R273H IgG-1

characteristic: External Id

text: VCU

text: public

text: E-MTAB-5653:R273H IgG-1

text: ArrayExpress

text: human

text: Protocols: ChIP-seq of H1299 cells stably transfected with empty vector (Vector) or the p53 mutant R273H and ChIP'd for p53 or IgG ChIP-seq of H1299 cells stably transfected with empty vector (Vector) or the p53 mutant R273H and ChIP'd for p53 or IgG

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: R273H IgG-1


E-MTAB-5653:R273H IgG-2

text: VCU

text: public

characteristic: SRA accession

text: E-MTAB-5653:R273H IgG-2

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: R273H IgG-2


E-MTAB-5653:R273H p53-1

text: VCU

text: public

text: E-MTAB-5653:R273H p53-1

characteristic: Submitter Id

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: R273H p53-1