text: SCAID

text: public

characteristic: collection date

text: Mtb isolate from the laboratory animal #51 infected with MTB-TB M. tuberculosis SCAID 187.0 (CP012506) on 60th day of treatment with antibiotics (74th day after infection).

text: Kazakhstan

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: human

characteristic: host scientific name

text: sputum

text: 48.00 N 68.00 E

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: Isolate 187.3.60.51 from MDR-TB infected guinea pig


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SCAID

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Mtb isolate from the laboratory animal #75 infected with MTB-TB M. tuberculosis SCAID 187.0 (CP012506) on 30th day of treatment with antibiotics and 2.5 mg/kg FS-1 (44th day after infection).

characteristic: description

text: Kazakhstan

text: diseased

text: human

characteristic: isolate

text: sputum

characteristic: isolation source

text: 48.00 N 68.00 E

characteristic: lat lon

text: Mycobacterium tuberculosis

characteristic: organism

text: Mycobacterium tuberculosis

text: Isolate 187.4.30.75 from MDR-TB infected guinea pig

characteristic: title


text: SCAID

text: public

characteristic: collection date

text: Mtb isolate from the laboratory animal #76 infected with MTB-TB M. tuberculosis SCAID 187.0 (CP012506) on 60th day of treatment with antibiotics and 2.5 mg/kg FS-1 (74th day after infection).

text: Kazakhstan

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: human

characteristic: host scientific name

text: sputum

text: 48.00 N 68.00 E

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: Isolate 187.4.60.76 from MDR-TB infected guinea pig


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SCAID

text: public

text: Mtb isolate from the laboratory animal #77 infected with MTB-TB M. tuberculosis SCAID 187.0 (CP012506) on 30th day of treatment with antibiotics and 2.5 mg/kg FS-1 (74th day after infection).

text: Kazakhstan

text: diseased

text: human

text: sputum

text: 48.00 N 68.00 E

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: Isolate 187.4.60.77 from MDR-TB infected guinea pig


text: SCAID

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Mtb isolate from the laboratory animal #104 infected with MTB-TB M. tuberculosis SCAID 187.0 (CP012506) on 30th day of treatment with antibiotics and 4.0 mg/kg FS-1 (44th day after infection).

text: Kazakhstan

text: diseased

text: human

text: sputum

text: 48.00 N 68.00 E

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: Isolate 187.5.30.104 from MDR-TB infected guinea pig


text: SCAID

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Mtb isolate from the laboratory animal #81 infected with MTB-TB M. tuberculosis SCAID 187.0 (CP012506) on 60th day of treatment with antibiotics and 4.0 mg/kg FS-1 (74th day after infection).

characteristic: description

text: Kazakhstan

text: diseased

text: human

characteristic: isolate

text: sputum

text: 48.00 N 68.00 E

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: Isolate 187.5.60.81.1 from MDR-TB infected guinea pig


text: SCAID

text: public

text: Kazakhstan

text: diseased

text: human

text: sputum

characteristic: isolation source

text: 48.00 N 68.00 E

characteristic: lat lon

text: Mycobacterium tuberculosis

characteristic: organism

text: Mycobacterium tuberculosis

text: Isolate 187.5.60.81.2 from MDR-TB infected guinea pig

characteristic: title


text: University of York

text: public

tag: Namespace:University of York

text: Escherichia coli

text: Escherichia coli

text: Novel ∆uvrD ∆rep synthetic lethality suppressor strain.


text: University of York

text: public

text: Escherichia coli

text: Escherichia coli

text: rpoB*35 ∆uvrD ∆rep synthetic lethality suppressor strain.


E-MTAB-4918:3-4h repl 1

text: public

text: E-MTAB-4918:3-4h repl 1

tag: Namespace:Max Planck Institute for Molecular Biomedicine

text: ArrayExpress

characteristic: broker name

text: mixed

characteristic: cell cycle phase

text: fruit fly

characteristic: common name

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: embryonic stage 8

characteristic: developmental stage

text: yw;EGFP-PCNA

characteristic: genotype

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: 3-4h repl 1

type: has member


E-MTAB-4918:3-4h repl 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Max Planck Institute for Molecular Biomedicine

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-4918:3-4h repl 2

text: ArrayExpress

text: mixed

text: fruit fly

text: embryonic stage 8

text: yw;EGFP-PCNA

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

text: 3-4h repl 2


E-MTAB-4918:3-4h repl 3

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-4918:3-4h repl 3

characteristic: Submitter Id

text: ArrayExpress

text: mixed

text: fruit fly

characteristic: description

text: embryonic stage 8

text: yw;EGFP-PCNA

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

text: 3-4h repl 3


name: E-MTAB-4918:mitotic nuclear cycle 1-4 repl 1

text: public

text: ArrayExpress

characteristic: broker name

text: M-phase

text: fruit fly

text: embryonic stage 1-4

text: yw;EGFP-PCNA

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

text: mitotic nuclear cycle 1-4 repl 1

characteristic: title


name: E-MTAB-4918:mitotic nuclear cycle 1-4 repl 2

text: public

text: ArrayExpress

text: M-phase

characteristic: cell cycle phase

text: fruit fly

characteristic: common name

text: embryonic stage 1-4

characteristic: developmental stage

text: yw;EGFP-PCNA

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

text: mitotic nuclear cycle 1-4 repl 2


E-MTAB-4918:nuclear cycle 12 repl 1

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-4918:nuclear cycle 12 repl 1

text: ArrayExpress

text: S-phase

text: fruit fly

text: nuclear cycle 12

text: yw;EGFP-PCNA

characteristic: genotype

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: nuclear cycle 12 repl 1


E-MTAB-4918:nuclear cycle 12 repl 2

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-4918:nuclear cycle 12 repl 2

text: ArrayExpress

text: S-phase

text: fruit fly

text: nuclear cycle 12

text: yw;EGFP-PCNA

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

text: nuclear cycle 12 repl 2


E-MTAB-4918:nuclear cycle 12 repl 3

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-4918:nuclear cycle 12 repl 3

text: ArrayExpress

text: S-phase

text: fruit fly

text: nuclear cycle 12

text: yw;EGFP-PCNA

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

text: nuclear cycle 12 repl 3


E-MTAB-4918:nuclear cycle 13 repl 1

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-4918:nuclear cycle 13 repl 1

characteristic: Submitter Id

text: ArrayExpress

text: S-phase

text: fruit fly

text: nuclear cycle 13

text: yw;EGFP-PCNA

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

text: nuclear cycle 13 repl 1


E-MTAB-4918:nuclear cycle 13 repl 2

text: public

text: E-MTAB-4918:nuclear cycle 13 repl 2

text: ArrayExpress

characteristic: broker name

text: S-phase

text: fruit fly

characteristic: description

text: nuclear cycle 13

text: yw;EGFP-PCNA

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

text: nuclear cycle 13 repl 2


E-MTAB-4918:nuclear cycle 13 repl 3

text: public

text: E-MTAB-4918:nuclear cycle 13 repl 3

text: ArrayExpress

text: S-phase

characteristic: cell cycle phase

text: fruit fly

characteristic: common name

text: nuclear cycle 13

text: yw;EGFP-PCNA

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

text: nuclear cycle 13 repl 3

characteristic: title


name: E-MTAB-4918:nuclear cycle 14 alpha-amanitin injected repl 1

characteristic: ENA-CHECKLIST

text: public

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. Immediately following collection, embryos were inspected under a fluorescent binocular and embryos that older than nuclear cycle 6 were discarded. For each batch, approximately 30-40 embryos were lined up individually on an agar block, transferred to a coverslip covered with heptane glue, air-dried for 3 min and covered with a drop of Voltalef 10S oil (VWR International). Injections were carried out using an Eppendorf Femtojet microinjection device. Alpha-amanitin (Sigma Aldrich) was dissolved in water at a concentration of 0.5 mg/ml. Each embryo was injected with approximately 0.2 nl of alpha-amanitin solution or water as a control. Given that the average volume of a Drosophila embryo is 15 nl17 and assuming that the injected material disperses evenly within the embryo, we expect a final concentration of approximately 6.6 μg/ml alpha-amanitin in the injected embryo. If embryos were older than nuclear cycle 8 at the time of injection they were discarded. After injection, embryos were incubated at 25°C and regularly monitored. Once the remaining embryos reached nuclear cycle 14, they were flushed off the coverslip using heptane and formaldehyde-fixed. 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

characteristic: developmental stage

text: yw;EGFP-PCNA

characteristic: genotype

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed


name: E-MTAB-4918:nuclear cycle 14 alpha-amanitin injected repl 2

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: S-phase

text: fruit fly

text: nuclear cycle 14

text: yw;EGFP-PCNA

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

characteristic: sex


name: E-MTAB-4918:nuclear cycle 14 alpha-amanitin injected repl 3

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: S-phase

text: fruit fly

text: nuclear cycle 14

text: yw;EGFP-PCNA

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed


name: E-MTAB-4918:nuclear cycle 14 alpha-amanitin injected repl 4

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: S-phase

text: fruit fly

text: nuclear cycle 14

text: yw;EGFP-PCNA

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed


E-MTAB-4918:nuclear cycle 14 repl 1

text: public

text: E-MTAB-4918:nuclear cycle 14 repl 1

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: S-phase

text: fruit fly

characteristic: description

text: nuclear cycle 14

text: yw;EGFP-PCNA

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

text: nuclear cycle 14 repl 1


E-MTAB-4918:nuclear cycle 14 repl 2

text: public

text: E-MTAB-4918:nuclear cycle 14 repl 2

text: ArrayExpress

text: S-phase

characteristic: cell cycle phase

text: fruit fly

characteristic: common name

text: nuclear cycle 14

text: yw;EGFP-PCNA

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

text: nuclear cycle 14 repl 2


E-MTAB-4918:nuclear cycle 14 repl 3

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-4918:nuclear cycle 14 repl 3

text: ArrayExpress

text: S-phase

text: fruit fly

text: nuclear cycle 14

characteristic: developmental stage

text: yw;EGFP-PCNA

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

text: nuclear cycle 14 repl 3

characteristic: title


name: E-MTAB-4918:nuclear cycle 14 water injected repl 1

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: S-phase

text: fruit fly

text: nuclear cycle 14

text: yw;EGFP-PCNA

characteristic: genotype

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

text: nuclear cycle 14 water injected repl 1


name: E-MTAB-4918:nuclear cycle 14 water injected repl 2

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: S-phase

text: fruit fly

text: nuclear cycle 14

text: yw;EGFP-PCNA

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: nuclear cycle 14 water injected repl 2


E-MTAB-4934:Control rep1

text: Institute of Parasitology

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-4934:Control rep1

tag: Namespace:Institute of Parasitology

text: ArrayExpress

text: Protocols: Previously constructed cell lines harboring MRB8170 and MRB4160 with modified TAP-tags, plus parental cell lines (29-13 cells) were collected after 48 hours of induction using tetracycline. All cell lines were grown in SDM-79 medium and were maintained in the exponential mid-log growth phase at 27°C. Protein extracts were prepared from UV-crosslinked (MRB8170, MRB4160 and MRP1) and control (UV crosslinked parental cell), and RNA was partially digested using low concentration of RNAse. RBP-RNA complexes were purified and subsequently visualized by 5’ end radiolabelling of RNAs. The complexes were size separated using denaturing gel electrophoresis and transferred to nitrocellulose membrane, Recovered RNA from the nitrocellulose membrane was reverse transcribed and size selected using denaturing gel electrophoresis. The size selected cDNA were further processed and PCR amplified (20 cycles) to obtain the iCLIP libraries. The library preparation was done according to the previously published protocol (Huppertz et al, Methods, 2014)

text: Procyclic stage

text: wild type genotype

characteristic: genetic modification

text: Trypanosoma brucei TREU927

text: Trypanosoma brucei brucei TREU927

text: Trypanosoma brucei brucei TREU927

text: Control rep1


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