text: EMBL Heidelberg

characteristic: INSDC center name

text: public

text: E-MTAB-4870:C1JDTACXX_12s008032_Pekowska_lane512s008032_ESC2

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate2

text: Mus musculus


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL Heidelberg

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-4870:C1JDTACXX_12s008032_Pekowska_lane512s008032_NSC1

tag: Namespace:EMBL Heidelberg

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: neural stem cell

characteristic: cell type

text: house mouse

characteristic: common name

text: Protocols: Buffers for the procedure, Lysis buffer: 10 mM HEPES pH=8, 10 mM NaCl, 0.2percent NP-40, Wash buffer: 50 mM Tris-HCl pH = 8, 50 mM NaCl, 1 mM EDTA, EZ-Link Iodoacetyl PEG2 Biotin resuspension buffer - EZ RB: 50 mM Tris-HCl, 5 mM EDTA, pH = 8 - 8.3, Dialysis buffer: 10 mM Tris HCl pH = 8, 1 mM EDTA, PBST: PBS, 0.01 percent of Tween, Beads wash buffer 10 mM Tris-HCl pH = 8, 50 mM NaCl, 0.4 percent Triton X-100, Klenow Wash Buffer: 50 mM Tris-HCl pH = 7.4, 0.4 percent Triton X-100, 0.1 mM EDTA, DNA extraction buffer: 50 mM Tris-HCl pH = 8, 0.2 percent SDS, 1 mM EDTA, 100 mM NaCl, DNA resuspension solution: 10 mM Tris-HCl pH = 8, Bind and Wash Buffer: 2x : 10 mM Tris-HCl pH = 7.5, 1mM EDTA, 2 M NaCl, Cell crossling protocol: Put 100 million cell pellet in 45 ml of fresh medium and add 1.25 ml of 37 percent formaldehyde, Incubate 10 min at RT, Add 2.5 ml of 2.5M glycine , Incubate 5 min at RT, Incubate 15 min on ice, Divide the cell mixture into 4 equal parts, Centrifuge at 1500 rpm for 5 min. at 4 degrees and store the pellets if needed. To start the TCC procedure, Lyse the cells in 550 ul lysis buffer completed with PIC using a homogenizer , Incubate on ice at least 15 minutes , Lyse the cells using the Dounce homogenizer by moving the pestile A up and down 10 times, Incubate on ice for 1 minutes , Apply 10 more strokes of the pestile, Transfer the sample to 2ml tube, Wash the cells twice with the wash buffer, spin conditions: 2500g for 5 minutes, V = 250 ul, Re suspend the cell pellet in 250 ul of wash buffer, Add 95 ul of 2percent SDS and incubate at 65 degreeC for 10 min, Prepare the EZ link Iodoacetyl-PEG2-Biotin For two reactions, Equilibrate the powder to RT to reduce humidification of the reagen, take 3 mg of the EZ link Iodoacetyl-PEG2-Biotin and re suspend in 220 ul of EZ RB in an amber tube, Cool the chromatin suspension to RT, Mix the suspension with 105ul of 25 mM EZlink Iodoacetyl-PEG2-Biotin (IPB), Rock at the room temperature for 1 hour, protect from light, Mix the chromatin with 1300 ul of 1x NEB Buffer 2, Incubate on ice for 5 minutes, Mix the sample with 225 ul of 10 percent triton X-100, Incubate on ice for 10 min , Incubate at 37degree C for 10 minutes, Now the sample is ready to be digested to this end, add, 100 ul of 10x NEB buffer 2, 350 ul of water, 5 ul of 1M DTT, 20 ul of HindIIII (100U/ul), dispose the sample to two tubes and incubate the digestion reaction OVN at 37 degreeC with overhead shaking.Place the mixture in a 20 kD cutoff Slide-A-Lyser Cassette, dialyse it against 1L of dialysis buffer for 3 hours, Renew the buffer and dialyze for an additional hour, Transfer the dialyzed sample (ca 2.5 ml) to a 15 ml falcon tube, During the last step, prepare the T1 beads. Take 400 ul of beads per chromatin sample, Wash the beads 3 times with PBST, Re suspend the beads in 2 ml of PBST, Divide the chromatin after dialysis into 5 equal parts, put them into 1.5 ml eppendorf tubes and add 400 ul of the above-mentioned bead suspension to these 5 aliquots of chromatin, Rock the chromatin with beads at RT for 30 minutes, During this time prepare the neutralized IPB solution - nIPB, take 0.750 mg IPB and add 52.5 ul of the resuspension buffer , add 7.75 mili-mols of bME - 9 ul of bME stock (14.3 Molar solution), Mix each aliquot of chromatin with 5 ul of nIPB, Incubate with rotation for 15 minutes at RT, Wash the beads once with 600 ul of TPBS, Wash the beads with 600 ul of Beads Wash Buffer, Re-suspend the beads in 100 ul of Beads Wash Buffer, add 69 ul of water, 1.1 ul of 1M MgCl2, 11 ul of 10x NEB buffer 2, 0.77 ul of 10 uM dATP, 0.77 ul of 10 uM dTTP, 0.77ul of 10 uM dGTPαS, 16.5 ul 0.4 mM Biotin-14-dCTP, 4.4 ul of 10 percent Triton-X100, 5 ul of 5U/ul Klenow. Fill in the overhangs by 40 minute rocking incubation at RT with 100 ul of the above-mentioned mix, After the incubation with Klenow add 5ul of 0.5 M EDTA to the suspension, Wash the beads twice with 600 ul of Klenow Wash Buffer, Re-suspend the beads in 500 ul of Klenow wash buffer and transfer them all in a new 50 ml falcon tube (V = 2.5 ml), Prepare the ligation mix (0.275 ul 10X NEB T4 Ligase buffer, 4.3 ml water, 198 ul 10percent triton X-100, 110 ul 1 M Tris-Hcl, pH=7.4, 55ul 10mg/ml BSA, 2ul Qucik Ligase NEB), Rock the mix for 4 hours at 16 degreeC , Stop the ligation by adding 200 ul of 0.5 M EDTA, Place the bead suspension on the magnet and aspirate the supernatant, Reverse the crosslinks: resuspend the beads in 400 ul of an extraction buffer, Add 20 ul of 20 mg/ml proteinase K, Incubate at 65 degreeC OVN , Add 5 ul of 20 mg/ml proteinase K, Incubate for 2 additional hours at 65 degreeC, Transfer the supernatant to a new tube and extract the DNA twice with, phenol : chloroform : isoamyl alcohol, Once with an equal volume of chloroform, Mix the resulting aqueous phase with , NaCl (final concentration: 200 mM), Glycogen (final concentration: 25 ug/ul), Add 900 ul of 98 percent ethanol, Incubate at -20 ovn or at -80 for 1 hour, Centrifuge for 20 minutes at 4 degreeC at max speed, Wash the pellet with 80 percent ethanol, Resuspend the pellet in 20 ul of DNA resuspension solution and pull the 5 samples, Mix the solution with 1 ul of RNase A and incubate for 30 minutes at 37 degreeC Isolate the DNA by phenol chloroform isolation and ethnol precipitation Resuspend the pellet in water. ExoIII treatment: take 5 ug of the purified DNA and resuspend it in a total volume of 90 ul of 1x NEB buffer 1 Add 300 U of ExoIII, Incubate for 1 hour at 37 degreeC, Stop the reaction by adding 2 ul of 0.5 M EDTA and 2 ul of 5 M NaCl, Incubate the reaction at 70 degreeC for 20 minutes, Add water to 100 ul and shear on Covaris S2 apparatus to an average size of 100-400 bp:, duty cycle: 5percent, intensity: 5, cycles/burst: 200, time: 180 seconds, Purify the DNA by Ampure bead solution, elute in 90 ul of water, End repair the sample for 30 minutes at 20 degrees: add 10 ul of 10x T4 ligase buffer supplemented with ATP and DTT, add 1.6 ul of 25 mM dNTP mix, 5 U of Klenow - 1ul, 15 U T4 polymerase - 5 ul, 50 U of PNK - 5ul, Purify the DNA by Quiaquick/Ampure beads, elute in 44 ul of water Add the A-overhangs incubate for 30 minutes at 37 degrees with :, add 5 ul of water, 5 ul of 10x NEB Buffer 2, 1 ul of 10 mM dATP solution , 3 ul of exo-Klenow, Stop the reaction by adding 1 ul of 0.5 EDTA, Wash 50 ul of MyOne Streptavidin C1 beads twice with 500 ul of 1x Wash and Bind buffer in DNA Lo-Bind tubes, Re suspend the beads in 50 ul of 2x, Wash and bind buffer, Mix the beads with the A-added DNA sample and rock the mixture for 30 min at RT, After the incubation, wash the beads once with 500 ul of supplemented bind Wash buffer., Wash the beads once in DNA resuspension solution, Now we would like to add sequencing adapters to this end re-suspend the beads in the following mix: 50 ul 2x rapid ligation mix, 3 ul of sequencing adapters (5uM), 47 ul of water, add 1 ul of rapid ligase, incubate at RT with mixing for 20 minutes, Stop the reaction by adding 6 ul of 0.5 M EDTA/100 ul of ligation mix, Wash the beads twice with 1x Bind and wash buffer, Wash the beads once with TE, Resuspend the beads in 30 ul of water Perform the PCR amplification and size excision. Prepare Phusion mix: 0.5 ul of primer, 5 ul of beads, 25 ul of Phusion MM, 19.5 ul of water. Buffers for the procedure, Lysis buffer: 10 mM HEPES pH=8, 10 mM NaCl, 0.2percent NP-40, Wash buffer: 50 mM Tris-HCl pH = 8, 50 mM NaCl, 1 mM EDTA, EZ-Link Iodoacetyl PEG2 Biotin resuspension buffer - EZ RB: 50 mM Tris-HCl, 5 mM EDTA, pH = 8 - 8.3, Dialysis buffer: 10 mM Tris HCl pH = 8, 1 mM EDTA, PBST: PBS, 0.01 percent of Tween, Beads wash buffer 10 mM Tris-HCl pH = 8, 50 mM NaCl, 0.4 percent Triton X-100, Klenow Wash Buffer: 50 mM Tris-HCl pH = 7.4, 0.4 percent Triton X-100, 0.1 mM EDTA, DNA extraction buffer: 50 mM Tris-HCl pH = 8, 0.2 percent SDS, 1 mM EDTA, 100 mM NaCl, DNA resuspension solution: 10 mM Tris-HCl pH = 8, Bind and Wash Buffer: 2x : 10 mM Tris-HCl pH = 7.5, 1mM EDTA, 2 M NaCl, Cell crossling protocol: Put 100 million cell pellet in 45 ml of fresh medium and add 1.25 ml of 37 percent formaldehyde, Incubate 10 min at RT, Add 2.5 ml of 2.5M glycine , Incubate 5 min at RT, Incubate 15 min on ice, Divide the cell mixture into 4 equal parts, Centrifuge at 1500 rpm for 5 min. at 4 degrees and store the pellets if needed. To start the TCC procedure, Lyse the cells in 550 ul lysis buffer completed with PIC using a homogenizer , Incubate on ice at least 15 minutes , Lyse the cells using the Dounce homogenizer by moving the pestile A up and down 10 times, Incubate on ice for 1 minutes , Apply 10 more strokes of the pestile, Transfer the sample to 2ml tube, Wash the cells twice with the wash buffer, spin conditions: 2500g for 5 minutes, V = 250 ul, Re suspend the cell pellet in 250 ul of wash buffer, Add 95 ul of 2percent SDS and incubate at 65 degreeC for 10 min, Prepare the EZ link Iodoacetyl-PEG2-Biotin For two reactions, Equilibrate the powder to RT to reduce humidification of the reagen, take 3 mg of the EZ link Iodoacetyl-PEG2-Biotin and re suspend in 220 ul of EZ RB in an amber tube, Cool the chromatin suspension to RT, Mix the suspension with 105ul of 25 mM EZlink Iodoacetyl-PEG2-Biotin (IPB), Rock at the room temperature for 1 hour, protect from light, Mix the chromatin with 1300 ul of 1x NEB Buffer 2, Incubate on ice for 5 minutes, Mix the sample with 225 ul of 10 percent triton X-100, Incubate on ice for 10 min , Incubate at 37degree C for 10 minutes, Now the sample is ready to be digested to this end, add, 100 ul of 10x NEB buffer 2, 350 ul of water, 5 ul of 1M DTT, 20 ul of HindIIII (100U/ul), dispose the sample to two tubes and incubate the digestion reaction OVN at 37 degreeC with overhead shaking.Place the mixture in a 20 kD cutoff Slide-A-Lyser Cassette, dialyse it against 1L of dialysis buffer for 3 hours, Renew the buffer and dialyze for an additional hour, Transfer the dialyzed sample (ca 2.5 ml) to a 15 ml falcon tube, During the last step, prepare the T1 beads. Take 400 ul of beads per chromatin sample, Wash the beads 3 times with PBST, Re suspend the beads in 2 ml of PBST, Divide the chromatin after dialysis into 5 equal parts, put them into 1.5 ml eppendorf tubes and add 400 ul of the above-mentioned bead suspension to these 5 aliquots of chromatin, Rock the chromatin with beads at RT for 30 minutes, During this time prepare the neutralized IPB solution - nIPB, take 0.750 mg IPB and add 52.5 ul of the resuspension buffer , add 7.75 mili-mols of bME - 9 ul of bME stock (14.3 Molar solution), Mix each aliquot of chromatin with 5 ul of nIPB, Incubate with rotation for 15 minutes at RT, Wash the beads once with 600 ul of TPBS, Wash the beads with 600 ul of Beads Wash Buffer, Re-suspend the beads in 100 ul of Beads Wash Buffer, add 69 ul of water, 1.1 ul of 1M MgCl2, 11 ul of 10x NEB buffer 2, 0.77 ul of 10 uM dATP, 0.77 ul of 10 uM dTTP, 0.77ul of 10 uM dGTPαS, 16.5 ul 0.4 mM Biotin-14-dCTP, 4.4 ul of 10 percent Triton-X100, 5 ul of 5U/ul Klenow. Fill in the overhangs by 40 minute rocking incubation at RT with 100 ul of the above-mentioned mix, After the incubation with Klenow add 5ul of 0.5 M EDTA to the suspension, Wash the beads twice with 600 ul of Klenow Wash Buffer, Re-suspend the beads in 500 ul of Klenow wash buffer and transfer them all in a new 50 ml falcon tube (V = 2.5 ml), Prepare the ligation mix (0.275 ul 10X NEB T4 Ligase buffer, 4.3 ml water, 198 ul 10percent triton X-100, 110 ul 1 M Tris-Hcl, pH=7.4, 55ul 10mg/ml BSA, 2ul Qucik Ligase NEB), Rock the mix for 4 hours at 16 degreeC , Stop the ligation by adding 200 ul of 0.5 M EDTA, Place the bead suspension on the magnet and aspirate the supernatant, Reverse the crosslinks: resuspend the beads in 400 ul of an extraction buffer, Add 20 ul of 20 mg/ml proteinase K, Incubate at 65 degreeC OVN , Add 5 ul of 20 mg/ml proteinase K, Incubate for 2 additional hours at 65 degreeC, Transfer the supernatant to a new tube and extract the DNA twice with, phenol : chloroform : isoamyl alcohol, Once with an equal volume of chloroform, Mix the resulting aqueous phase with , NaCl (final concentration: 200 mM), Glycogen (final concentration: 25 ug/ul), Add 900 ul of 98 percent ethanol, Incubate at -20 ovn or at -80 for 1 hour, Centrifuge for 20 minutes at 4 degreeC at max speed, Wash the pellet with 80 percent ethanol, Resuspend the pellet in 20 ul of DNA resuspension solution and pull the 5 samples, Mix the solution with 1 ul of RNase A and incubate for 30 minutes at 37 degreeC Isolate the DNA by phenol chloroform isolation and ethnol precipitation Resuspend the pellet in water. ExoIII treatment: take 5 ug of the purified DNA and resuspend it in a total volume of 90 ul of 1x NEB buffer 1 Add 300 U of ExoIII, Incubate for 1 hour at 37 degreeC, Stop the reaction by adding 2 ul of 0.5 M EDTA and 2 ul of 5 M NaCl, Incubate the reaction at 70 degreeC for 20 minutes, Add water to 100 ul and shear on Covaris S2 apparatus to an average size of 100-400 bp:, duty cycle: 5percent, intensity: 5, cycles/burst: 200, time: 180 seconds, Purify the DNA by Ampure bead solution, elute in 90 ul of water, End repair the sample for 30 minutes at 20 degrees: add 10 ul of 10x T4 ligase buffer supplemented with ATP and DTT, add 1.6 ul of 25 mM dNTP mix, 5 U of Klenow - 1ul, 15 U T4 polymerase - 5 ul, 50 U of PNK - 5ul, Purify the DNA by Quiaquick/Ampure beads, elute in 44 ul of water Add the A-overhangs incubate for 30 minutes at 37 degrees with :, add 5 ul of water, 5 ul of 10x NEB Buffer 2, 1 ul of 10 mM dATP solution , 3 ul of exo-Klenow, Stop the reaction by adding 1 ul of 0.5 EDTA, Wash 50 ul of MyOne Streptavidin C1 beads twice with 500 ul of 1x Wash and Bind buffer in DNA Lo-Bind tubes, Re suspend the beads in 50 ul of 2x, Wash and bind buffer, Mix the beads with the A-added DNA sample and rock the mixture for 30 min at RT, After the incubation, wash the beads once with 500 ul of supplemented bind Wash buffer., Wash the beads once in DNA resuspension solution, Now we would like to add sequencing adapters to this end re-suspend the beads in the following mix: 50 ul 2x rapid ligation mix, 3 ul of sequencing adapters (5uM), 47 ul of water, add 1 ul of rapid ligase, incubate at RT with mixing for 20 minutes, Stop the reaction by adding 6 ul of 0.5 M EDTA/100 ul of ligation mix, Wash the beads twice with 1x Bind and wash buffer, Wash the beads once with TE, Resuspend the beads in 30 ul of water Perform the PCR amplification and size excision. Prepare Phusion mix: 0.5 ul of primer, 5 ul of beads, 25 ul of Phusion MM, 19.5 ul of water.

characteristic: description

text: Mus musculus

characteristic: organism

text: Mus musculus

text: biological replicate1

characteristic: replicate

text: Mus musculus

characteristic: title


text: EMBL Heidelberg

characteristic: INSDC center name

text: public

text: E-MTAB-4870:C1JDTACXX_12s008032_Pekowska_lane512s008032_NSC2

text: ArrayExpress

text: neural stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate2

text: Mus musculus


characteristic: ENA-CHECKLIST

text: EMBL Heidelberg

text: public

text: E-MTAB-4870:C1JDTACXX_12s008032_Pekowska_lane612s008032_ESC1

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate1

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

text: EMBL Heidelberg

text: public

text: E-MTAB-4870:C1JDTACXX_12s008032_Pekowska_lane612s008032_ESC2

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate2

text: Mus musculus


characteristic: ENA-LAST-UPDATE

text: EMBL Heidelberg

text: public

text: E-MTAB-4870:C1JDTACXX_12s008032_Pekowska_lane612s008032_NSC1

text: ArrayExpress

text: neural stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate1

text: Mus musculus


characteristic: External Id

text: EMBL Heidelberg

text: public

text: E-MTAB-4870:C1JDTACXX_12s008032_Pekowska_lane612s008032_NSC2

text: ArrayExpress

text: neural stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate2

text: Mus musculus


text: EMBL Heidelberg

characteristic: INSDC first public

text: public

text: E-MTAB-4870:C1JDTACXX_12s008032_Pekowska_lane712s008032_ESC1

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate1

text: Mus musculus


text: EMBL Heidelberg

characteristic: INSDC last update

text: public

text: E-MTAB-4870:C1JDTACXX_12s008032_Pekowska_lane712s008032_ESC2

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate2

text: Mus musculus


text: EMBL Heidelberg

text: public

characteristic: INSDC status

text: E-MTAB-4870:C1JDTACXX_12s008032_Pekowska_lane712s008032_NSC1

text: ArrayExpress

text: neural stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate1

text: Mus musculus


text: EMBL Heidelberg

text: public

characteristic: SRA accession

text: E-MTAB-4870:C1JDTACXX_12s008032_Pekowska_lane712s008032_NSC2

text: ArrayExpress

text: neural stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate2

text: Mus musculus


text: EMBL Heidelberg

text: public

text: E-MTAB-4870:C1JDTACXX_12s008032_Pekowska_lane812s008032_ESC1

characteristic: Submitter Id

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate1

text: Mus musculus


text: EMBL Heidelberg

text: public

text: E-MTAB-4870:C1JDTACXX_12s008032_Pekowska_lane812s008032_ESC2

text: ArrayExpress

characteristic: broker name

text: embryonic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate2

text: Mus musculus


text: EMBL Heidelberg

text: public

text: E-MTAB-4870:C1JDTACXX_12s008032_Pekowska_lane812s008032_NSC1

text: ArrayExpress

text: neural stem cell

characteristic: cell type

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate1

text: Mus musculus


text: EMBL Heidelberg

text: public

text: E-MTAB-4870:C1JDTACXX_12s008032_Pekowska_lane812s008032_NSC2

text: ArrayExpress

text: neural stem cell

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

text: biological replicate1

text: Mus musculus


text: EMBL Heidelberg

text: public

text: E-MTAB-4870:C34M8ACXX_15s009462_Pekowska_lane215s009462_ESC1_2i

text: ArrayExpress

text: embryonic stem cell

text: house mouse

characteristic: description

text: Mus musculus

text: Mus musculus

text: biological replicate1

text: Mus musculus


text: EMBL Heidelberg

text: public

text: E-MTAB-4870:C34M8ACXX_15s009463_Pekowska_lane315s009463_ESC2_2i

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus

text: biological replicate2

text: Mus musculus


text: EMBL Heidelberg

text: public

text: E-MTAB-4870:C799JACXX_15s013537_Pekowska_EpiSC1

text: ArrayExpress

text: epiblast-derived stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate1

characteristic: replicate

text: Mus musculus


text: EMBL Heidelberg

text: public

text: E-MTAB-4870:C799JACXX_15s013538_Pekowska_EpiSC2

text: ArrayExpress

text: epiblast-derived stem cell

text: house mouse

text: Protocols: Buffers for the procedure, Lysis buffer: 10 mM HEPES pH=8, 10 mM NaCl, 0.2percent NP-40, Wash buffer: 50 mM Tris-HCl pH = 8, 50 mM NaCl, 1 mM EDTA, EZ-Link Iodoacetyl PEG2 Biotin resuspension buffer - EZ RB: 50 mM Tris-HCl, 5 mM EDTA, pH = 8 - 8.3, Dialysis buffer: 10 mM Tris HCl pH = 8, 1 mM EDTA, PBST: PBS, 0.01 percent of Tween, Beads wash buffer 10 mM Tris-HCl pH = 8, 50 mM NaCl, 0.4 percent Triton X-100, Klenow Wash Buffer: 50 mM Tris-HCl pH = 7.4, 0.4 percent Triton X-100, 0.1 mM EDTA, DNA extraction buffer: 50 mM Tris-HCl pH = 8, 0.2 percent SDS, 1 mM EDTA, 100 mM NaCl, DNA resuspension solution: 10 mM Tris-HCl pH = 8, Bind and Wash Buffer: 2x : 10 mM Tris-HCl pH = 7.5, 1mM EDTA, 2 M NaCl, Cell crossling protocol: Put 100 million cell pellet in 45 ml of fresh medium and add 1.25 ml of 37 percent formaldehyde, Incubate 10 min at RT, Add 2.5 ml of 2.5M glycine , Incubate 5 min at RT, Incubate 15 min on ice, Divide the cell mixture into 4 equal parts, Centrifuge at 1500 rpm for 5 min. at 4 degrees and store the pellets if needed. To start the TCC procedure, Lyse the cells in 550 ul lysis buffer completed with PIC using a homogenizer , Incubate on ice at least 15 minutes , Lyse the cells using the Dounce homogenizer by moving the pestile A up and down 10 times, Incubate on ice for 1 minutes , Apply 10 more strokes of the pestile, Transfer the sample to 2ml tube, Wash the cells twice with the wash buffer, spin conditions: 2500g for 5 minutes, V = 250 ul, Re suspend the cell pellet in 250 ul of wash buffer, Add 95 ul of 2percent SDS and incubate at 65 degreeC for 10 min, Prepare the EZ link Iodoacetyl-PEG2-Biotin For two reactions, Equilibrate the powder to RT to reduce humidification of the reagen, take 3 mg of the EZ link Iodoacetyl-PEG2-Biotin and re suspend in 220 ul of EZ RB in an amber tube, Cool the chromatin suspension to RT, Mix the suspension with 105ul of 25 mM EZlink Iodoacetyl-PEG2-Biotin (IPB), Rock at the room temperature for 1 hour, protect from light, Mix the chromatin with 1300 ul of 1x NEB Buffer 2, Incubate on ice for 5 minutes, Mix the sample with 225 ul of 10 percent triton X-100, Incubate on ice for 10 min , Incubate at 37degree C for 10 minutes, Now the sample is ready to be digested to this end, add, 100 ul of 10x NEB buffer 2, 350 ul of water, 5 ul of 1M DTT, 20 ul of HindIIII (100U/ul), dispose the sample to two tubes and incubate the digestion reaction OVN at 37 degreeC with overhead shaking.Place the mixture in a 20 kD cutoff Slide-A-Lyser Cassette, dialyse it against 1L of dialysis buffer for 3 hours, Renew the buffer and dialyze for an additional hour, Transfer the dialyzed sample (ca 2.5 ml) to a 15 ml falcon tube, During the last step, prepare the T1 beads. Take 400 ul of beads per chromatin sample, Wash the beads 3 times with PBST, Re suspend the beads in 2 ml of PBST, Divide the chromatin after dialysis into 5 equal parts, put them into 1.5 ml eppendorf tubes and add 400 ul of the above-mentioned bead suspension to these 5 aliquots of chromatin, Rock the chromatin with beads at RT for 30 minutes, During this time prepare the neutralized IPB solution - nIPB, take 0.750 mg IPB and add 52.5 ul of the resuspension buffer , add 7.75 mili-mols of bME - 9 ul of bME stock (14.3 Molar solution), Mix each aliquot of chromatin with 5 ul of nIPB, Incubate with rotation for 15 minutes at RT, Wash the beads once with 600 ul of TPBS, Wash the beads with 600 ul of Beads Wash Buffer, Re-suspend the beads in 100 ul of Beads Wash Buffer, add 69 ul of water, 1.1 ul of 1M MgCl2, 11 ul of 10x NEB buffer 2, 0.77 ul of 10 uM dATP, 0.77 ul of 10 uM dTTP, 0.77ul of 10 uM dGTPαS, 16.5 ul 0.4 mM Biotin-14-dCTP, 4.4 ul of 10 percent Triton-X100, 5 ul of 5U/ul Klenow. Fill in the overhangs by 40 minute rocking incubation at RT with 100 ul of the above-mentioned mix, After the incubation with Klenow add 5ul of 0.5 M EDTA to the suspension, Wash the beads twice with 600 ul of Klenow Wash Buffer, Re-suspend the beads in 500 ul of Klenow wash buffer and transfer them all in a new 50 ml falcon tube (V = 2.5 ml), Prepare the ligation mix (0.275 ul 10X NEB T4 Ligase buffer, 4.3 ml water, 198 ul 10percent triton X-100, 110 ul 1 M Tris-Hcl, pH=7.4, 55ul 10mg/ml BSA, 2ul Qucik Ligase NEB), Rock the mix for 4 hours at 16 degreeC , Stop the ligation by adding 200 ul of 0.5 M EDTA, Place the bead suspension on the magnet and aspirate the supernatant, Reverse the crosslinks: resuspend the beads in 400 ul of an extraction buffer, Add 20 ul of 20 mg/ml proteinase K, Incubate at 65 degreeC OVN , Add 5 ul of 20 mg/ml proteinase K, Incubate for 2 additional hours at 65 degreeC, Transfer the supernatant to a new tube and extract the DNA twice with, phenol : chloroform : isoamyl alcohol, Once with an equal volume of chloroform, Mix the resulting aqueous phase with , NaCl (final concentration: 200 mM), Glycogen (final concentration: 25 ug/ul), Add 900 ul of 98 percent ethanol, Incubate at -20 ovn or at -80 for 1 hour, Centrifuge for 20 minutes at 4 degreeC at max speed, Wash the pellet with 80 percent ethanol, Resuspend the pellet in 20 ul of DNA resuspension solution and pull the 5 samples, Mix the solution with 1 ul of RNase A and incubate for 30 minutes at 37 degreeC Isolate the DNA by phenol chloroform isolation and ethnol precipitation Resuspend the pellet in water. ExoIII treatment: take 5 ug of the purified DNA and resuspend it in a total volume of 90 ul of 1x NEB buffer 1 Add 300 U of ExoIII, Incubate for 1 hour at 37 degreeC, Stop the reaction by adding 2 ul of 0.5 M EDTA and 2 ul of 5 M NaCl, Incubate the reaction at 70 degreeC for 20 minutes, Add water to 100 ul and shear on Covaris S2 apparatus to an average size of 100-400 bp:, duty cycle: 5percent, intensity: 5, cycles/burst: 200, time: 180 seconds, Purify the DNA by Ampure bead solution, elute in 90 ul of water, End repair the sample for 30 minutes at 20 degrees: add 10 ul of 10x T4 ligase buffer supplemented with ATP and DTT, add 1.6 ul of 25 mM dNTP mix, 5 U of Klenow - 1ul, 15 U T4 polymerase - 5 ul, 50 U of PNK - 5ul, Purify the DNA by Quiaquick/Ampure beads, elute in 44 ul of water Add the A-overhangs incubate for 30 minutes at 37 degrees with :, add 5 ul of water, 5 ul of 10x NEB Buffer 2, 1 ul of 10 mM dATP solution , 3 ul of exo-Klenow, Stop the reaction by adding 1 ul of 0.5 EDTA, Wash 50 ul of MyOne Streptavidin C1 beads twice with 500 ul of 1x Wash and Bind buffer in DNA Lo-Bind tubes, Re suspend the beads in 50 ul of 2x, Wash and bind buffer, Mix the beads with the A-added DNA sample and rock the mixture for 30 min at RT, After the incubation, wash the beads once with 500 ul of supplemented bind Wash buffer., Wash the beads once in DNA resuspension solution, Now we would like to add sequencing adapters to this end re-suspend the beads in the following mix: 50 ul 2x rapid ligation mix, 3 ul of sequencing adapters (5uM), 47 ul of water, add 1 ul of rapid ligase, incubate at RT with mixing for 20 minutes, Stop the reaction by adding 6 ul of 0.5 M EDTA/100 ul of ligation mix, Wash the beads twice with 1x Bind and wash buffer, Wash the beads once with TE, Resuspend the beads in 30 ul of water Perform the PCR amplification and size excision. Prepare Phusion mix: 0.5 ul of primer, 5 ul of beads, 25 ul of Phusion MM, 19.5 ul of water. Buffers for the procedure, Lysis buffer: 10 mM HEPES pH=8, 10 mM NaCl, 0.2percent NP-40, Wash buffer: 50 mM Tris-HCl pH = 8, 50 mM NaCl, 1 mM EDTA, EZ-Link Iodoacetyl PEG2 Biotin resuspension buffer - EZ RB: 50 mM Tris-HCl, 5 mM EDTA, pH = 8 - 8.3, Dialysis buffer: 10 mM Tris HCl pH = 8, 1 mM EDTA, PBST: PBS, 0.01 percent of Tween, Beads wash buffer 10 mM Tris-HCl pH = 8, 50 mM NaCl, 0.4 percent Triton X-100, Klenow Wash Buffer: 50 mM Tris-HCl pH = 7.4, 0.4 percent Triton X-100, 0.1 mM EDTA, DNA extraction buffer: 50 mM Tris-HCl pH = 8, 0.2 percent SDS, 1 mM EDTA, 100 mM NaCl, DNA resuspension solution: 10 mM Tris-HCl pH = 8, Bind and Wash Buffer: 2x : 10 mM Tris-HCl pH = 7.5, 1mM EDTA, 2 M NaCl, Cell crossling protocol: Put 100 million cell pellet in 45 ml of fresh medium and add 1.25 ml of 37 percent formaldehyde, Incubate 10 min at RT, Add 2.5 ml of 2.5M glycine , Incubate 5 min at RT, Incubate 15 min on ice, Divide the cell mixture into 4 equal parts, Centrifuge at 1500 rpm for 5 min. at 4 degrees and store the pellets if needed. To start the TCC procedure, Lyse the cells in 550 ul lysis buffer completed with PIC using a homogenizer , Incubate on ice at least 15 minutes , Lyse the cells using the Dounce homogenizer by moving the pestile A up and down 10 times, Incubate on ice for 1 minutes , Apply 10 more strokes of the pestile, Transfer the sample to 2ml tube, Wash the cells twice with the wash buffer, spin conditions: 2500g for 5 minutes, V = 250 ul, Re suspend the cell pellet in 250 ul of wash buffer, Add 95 ul of 2percent SDS and incubate at 65 degreeC for 10 min, Prepare the EZ link Iodoacetyl-PEG2-Biotin For two reactions, Equilibrate the powder to RT to reduce humidification of the reagen, take 3 mg of the EZ link Iodoacetyl-PEG2-Biotin and re suspend in 220 ul of EZ RB in an amber tube, Cool the chromatin suspension to RT, Mix the suspension with 105ul of 25 mM EZlink Iodoacetyl-PEG2-Biotin (IPB), Rock at the room temperature for 1 hour, protect from light, Mix the chromatin with 1300 ul of 1x NEB Buffer 2, Incubate on ice for 5 minutes, Mix the sample with 225 ul of 10 percent triton X-100, Incubate on ice for 10 min , Incubate at 37degree C for 10 minutes, Now the sample is ready to be digested to this end, add, 100 ul of 10x NEB buffer 2, 350 ul of water, 5 ul of 1M DTT, 20 ul of HindIIII (100U/ul), dispose the sample to two tubes and incubate the digestion reaction OVN at 37 degreeC with overhead shaking.Place the mixture in a 20 kD cutoff Slide-A-Lyser Cassette, dialyse it against 1L of dialysis buffer for 3 hours, Renew the buffer and dialyze for an additional hour, Transfer the dialyzed sample (ca 2.5 ml) to a 15 ml falcon tube, During the last step, prepare the T1 beads. Take 400 ul of beads per chromatin sample, Wash the beads 3 times with PBST, Re suspend the beads in 2 ml of PBST, Divide the chromatin after dialysis into 5 equal parts, put them into 1.5 ml eppendorf tubes and add 400 ul of the above-mentioned bead suspension to these 5 aliquots of chromatin, Rock the chromatin with beads at RT for 30 minutes, During this time prepare the neutralized IPB solution - nIPB, take 0.750 mg IPB and add 52.5 ul of the resuspension buffer , add 7.75 mili-mols of bME - 9 ul of bME stock (14.3 Molar solution), Mix each aliquot of chromatin with 5 ul of nIPB, Incubate with rotation for 15 minutes at RT, Wash the beads once with 600 ul of TPBS, Wash the beads with 600 ul of Beads Wash Buffer, Re-suspend the beads in 100 ul of Beads Wash Buffer, add 69 ul of water, 1.1 ul of 1M MgCl2, 11 ul of 10x NEB buffer 2, 0.77 ul of 10 uM dATP, 0.77 ul of 10 uM dTTP, 0.77ul of 10 uM dGTPαS, 16.5 ul 0.4 mM Biotin-14-dCTP, 4.4 ul of 10 percent Triton-X100, 5 ul of 5U/ul Klenow. Fill in the overhangs by 40 minute rocking incubation at RT with 100 ul of the above-mentioned mix, After the incubation with Klenow add 5ul of 0.5 M EDTA to the suspension, Wash the beads twice with 600 ul of Klenow Wash Buffer, Re-suspend the beads in 500 ul of Klenow wash buffer and transfer them all in a new 50 ml falcon tube (V = 2.5 ml), Prepare the ligation mix (0.275 ul 10X NEB T4 Ligase buffer, 4.3 ml water, 198 ul 10percent triton X-100, 110 ul 1 M Tris-Hcl, pH=7.4, 55ul 10mg/ml BSA, 2ul Qucik Ligase NEB), Rock the mix for 4 hours at 16 degreeC , Stop the ligation by adding 200 ul of 0.5 M EDTA, Place the bead suspension on the magnet and aspirate the supernatant, Reverse the crosslinks: resuspend the beads in 400 ul of an extraction buffer, Add 20 ul of 20 mg/ml proteinase K, Incubate at 65 degreeC OVN , Add 5 ul of 20 mg/ml proteinase K, Incubate for 2 additional hours at 65 degreeC, Transfer the supernatant to a new tube and extract the DNA twice with, phenol : chloroform : isoamyl alcohol, Once with an equal volume of chloroform, Mix the resulting aqueous phase with , NaCl (final concentration: 200 mM), Glycogen (final concentration: 25 ug/ul), Add 900 ul of 98 percent ethanol, Incubate at -20 ovn or at -80 for 1 hour, Centrifuge for 20 minutes at 4 degreeC at max speed, Wash the pellet with 80 percent ethanol, Resuspend the pellet in 20 ul of DNA resuspension solution and pull the 5 samples, Mix the solution with 1 ul of RNase A and incubate for 30 minutes at 37 degreeC Isolate the DNA by phenol chloroform isolation and ethnol precipitation Resuspend the pellet in water. ExoIII treatment: take 5 ug of the purified DNA and resuspend it in a total volume of 90 ul of 1x NEB buffer 1 Add 300 U of ExoIII, Incubate for 1 hour at 37 degreeC, Stop the reaction by adding 2 ul of 0.5 M EDTA and 2 ul of 5 M NaCl, Incubate the reaction at 70 degreeC for 20 minutes, Add water to 100 ul and shear on Covaris S2 apparatus to an average size of 100-400 bp:, duty cycle: 5percent, intensity: 5, cycles/burst: 200, time: 180 seconds, Purify the DNA by Ampure bead solution, elute in 90 ul of water, End repair the sample for 30 minutes at 20 degrees: add 10 ul of 10x T4 ligase buffer supplemented with ATP and DTT, add 1.6 ul of 25 mM dNTP mix, 5 U of Klenow - 1ul, 15 U T4 polymerase - 5 ul, 50 U of PNK - 5ul, Purify the DNA by Quiaquick/Ampure beads, elute in 44 ul of water Add the A-overhangs incubate for 30 minutes at 37 degrees with :, add 5 ul of water, 5 ul of 10x NEB Buffer 2, 1 ul of 10 mM dATP solution , 3 ul of exo-Klenow, Stop the reaction by adding 1 ul of 0.5 EDTA, Wash 50 ul of MyOne Streptavidin C1 beads twice with 500 ul of 1x Wash and Bind buffer in DNA Lo-Bind tubes, Re suspend the beads in 50 ul of 2x, Wash and bind buffer, Mix the beads with the A-added DNA sample and rock the mixture for 30 min at RT, After the incubation, wash the beads once with 500 ul of supplemented bind Wash buffer., Wash the beads once in DNA resuspension solution, Now we would like to add sequencing adapters to this end re-suspend the beads in the following mix: 50 ul 2x rapid ligation mix, 3 ul of sequencing adapters (5uM), 47 ul of water, add 1 ul of rapid ligase, incubate at RT with mixing for 20 minutes, Stop the reaction by adding 6 ul of 0.5 M EDTA/100 ul of ligation mix, Wash the beads twice with 1x Bind and wash buffer, Wash the beads once with TE, Resuspend the beads in 30 ul of water Perform the PCR amplification and size excision. Prepare Phusion mix: 0.5 ul of primer, 5 ul of beads, 25 ul of Phusion MM, 19.5 ul of water.

text: Mus musculus

text: Mus musculus

text: biological replicate2

text: Mus musculus

characteristic: title


text: EMBL Heidelberg

characteristic: INSDC center name

text: public

text: E-MTAB-4870:C7AP3ACXX_15s012980_Pekowska_lane415s012980_EpiSC1

text: ArrayExpress

text: epiblast-derived stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate1

text: Mus musculus


characteristic: ENA-CHECKLIST

text: EMBL Heidelberg

text: public

text: E-MTAB-4870:C7AP3ACXX_15s012980_Pekowska_lane515s012981_EpiSC2

text: ArrayExpress

text: epiblast-derived stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate2

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

text: EMBL Heidelberg

text: public

text: E-MTAB-4870:D179FACXX_12s006436_Pekowska_lane812s006436_ESC1

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate1

text: Mus musculus


characteristic: ENA-LAST-UPDATE

text: EMBL Heidelberg

text: public

text: E-MTAB-4870:D179FACXX_12s006436_Pekowska_lane812s006436_ESC2

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate2

text: Mus musculus


characteristic: External Id

text: EMBL Heidelberg

text: public

text: E-MTAB-4870:D179FACXX_12s006436_Pekowska_lane812s006436_NSC1

text: ArrayExpress

text: neural stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate1

text: Mus musculus


text: EMBL Heidelberg

characteristic: INSDC first public

text: public

text: E-MTAB-4870:D179FACXX_12s006436_Pekowska_lane812s006436_NSC2

text: ArrayExpress

text: neural stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate2

text: Mus musculus


text: EMBL Heidelberg

characteristic: INSDC last update

text: public

text: E-MTAB-4870:D1GUAACXX_12s007362_Pekowska_lane212s007362_ESC1

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate1

text: Mus musculus


text: EMBL Heidelberg

text: public

characteristic: INSDC status

text: E-MTAB-4870:D1GUAACXX_12s007362_Pekowska_lane212s007362_ESC2

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate2

text: Mus musculus


text: EMBL Heidelberg

text: public

characteristic: SRA accession

text: E-MTAB-4870:D1GUAACXX_12s007362_Pekowska_lane212s007362_NSC1

text: ArrayExpress

text: neural stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate1

text: Mus musculus


text: EMBL Heidelberg

text: public

text: E-MTAB-4870:D1GUAACXX_12s007362_Pekowska_lane212s007362_NSC2

characteristic: Submitter Id

text: ArrayExpress

text: neural stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: biological replicate2

text: Mus musculus


text: JLU

text: public

characteristic: collection date

text: Brucella sp. 10RB9215 sequencing

text: Tanzania

characteristic: geographic location (country and/or sea)

text: African bull frog, Pyxicephalus edulis

characteristic: host

text: Brucella sp. 10RB9215

text: Brucella sp. 10RB9215

text: Brucella sp. 10RB9215 sequencing


text: CEBITEC

text: public

text: Draft genome sequence of Xanthomonas translucens pv. graminis ART-Xtg2

characteristic: description

text: grass

characteristic: environment (biome)

text: grass

characteristic: environment (feature)

text: grass

characteristic: environment (material)

text: Switzerland

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

characteristic: isolate

text: Xanthomonas translucens pv. graminis

text: plant-associated

characteristic: plant-associated environmental package

characteristic: project name

text: Xanthomonas translucens pv. graminis

text: Illumina MiSeq

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CEBITEC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Draft genome sequence of Xanthomonas translucens pv. graminis ART-Xtg9

text: grass

text: grass

text: grass

text: Switzerland

text: mimarks-survey

text: Xanthomonas translucens pv. graminis

characteristic: organism

text: plant-associated

text: Xanthomonas translucens pv. graminis

text: Illumina MiSeq

characteristic: title


E-MTAB-4884:Sample 1

text: Dept of Neurological surgerz, UCSF

text: public

characteristic: SRA accession

text: E-MTAB-4884:Sample 1

tag: Namespace:Dept of Neurological surgerz, UCSF

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: mesenchymal stroma cell

characteristic: cell type

text: human

characteristic: common name

text: Protocols: Human mesenchymal stromal-cells were obtained from bone marrows of three donors, recruited via the Bone-Marrow Transplant Program of the Hematology Service at Reina Sofia University Hospital (Cordoba, Spain). All of them signed written informed-consent. MSC isolation, characterization and storage were performed as we have previously described (Casado-Diaz et al., 2008) MSC were cultured in 75 cm2 flasks from Nunc (Kamstrupvej, Denmark), containing 12 ml Minimum Essential-Medium Alpha (MEM ) Eagle from Lonza (Basel, Switzerland), supplemented with 10% fetal bovine-serum (FBS) from Gibco - Life Technologies - Thermo Fisher Scientific (Waltham, MA, USA), 2 mM UltraGlutamine (Lonza), 1 ng basic fibroblast-growth factor (bFGF)/ml from Sigma-Aldrich (Saint Louis, MO, USA), 100 U ampicillin and 0.1 mg streptomycin/ml. Cells were grown in an incubator at 37 oC with 5% CO2 and humidity, until about 80 to 90% confluence. Then, cultures were maintained in such medium without bFGF (controls) or likewise but supplemented with 5x107 M dexamethasone, 0.5 mM isobutylmethylxanthine and 50 mM indomethacin (Sigma-Aldrich) inducing agents to trigger differentiation into adipocytes. Adipogenic differentiation at day 14 was determined by oil red-O staining of lipid droplets (LD). Then, cells were fixed with 3.7% formaldehyde for 10 min, washed with isopropanol (60% in water) and stained for 15-20 min with a mixture of 8.2 ml of 0.3% (w/v in isopropanol) of oil red-O plus 6.8 ml of distilled water. They were then washed with water, stained with hematoxylin and visualized under a light microscope (all chemicals from Sigma-Aldrich). Total RNA were isolated from both control and induced-to-differentiate cultures with mirVana miRNA Isolation Kit from Ambion - Life Technologies - Thermo Fisher Scientific, at days seven and 14 after adipogenesis induction. RNA were quantified using a ND-1000 spectrophotometer from NanoDrop - Thermo Fisher Scientific, and their integrity checked by agarose-gel electrophoresis (AGE). RNA samples were pooled from each time and donor, to generate two samples: control (RNA pooled from days seven and 14) and cells induced into adipocytes (RNA pooled from days seven and 14) for subsequent downstream analyses. ST-DGE genome-wide transcription profilings were performed with 5 g total RNA input, as we have previously described (Molina et al., 2011; Zawada et al., 2011), using TrueQuant technology from GenXPro (Frankfurt Main, Germany), in order to identify Polymerase Chain-Reaction (PCR)-derived copies in the dataset, as we have reported (Muller et al., 2014). Populations of small RNA (17 to 30 b) were size-selected from total RNA using flashPAGE Fractionator System from Ambion - Life Technologies - Thermo Fisher Scientific, for preparation of miRNA libraries.

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

characteristic: stimulus

text: Sample 1

type: has member


E-MTAB-4884:Sample 2

characteristic: ENA-CHECKLIST

text: Dept of Neurological surgerz, UCSF

text: public

text: E-MTAB-4884:Sample 2

text: ArrayExpress

text: mesenchymal stroma cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: 5x107 M dexamethasone, 0.5 mM isobutylmethylxanthine and 50 mM indomethacin

text: Sample 2


E-MTAB-4884:Sample 3

characteristic: ENA-FIRST-PUBLIC

text: Dept of Neurological surgerz, UCSF

text: public

text: E-MTAB-4884:Sample 3

text: ArrayExpress

text: mesenchymal stroma cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Unstimulated

text: Sample 3


E-MTAB-4884:Sample 4

characteristic: ENA-LAST-UPDATE

text: Dept of Neurological surgerz, UCSF

text: public

text: E-MTAB-4884:Sample 4

text: ArrayExpress

text: mesenchymal stroma cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Unstimulated

text: Sample 4


characteristic: External Id

text: WTCMP

text: public

text: Trypanosoma brucei brucei

text: Trypanosoma brucei brucei

text: Lister 427

characteristic: strain

text: Cell-cycle sorted T. brucei cells blood stream form earlyS


text: WTCMP

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Trypanosoma brucei brucei

text: Trypanosoma brucei brucei

text: Lister 427

text: Cell-cycle sorted T. brucei cells blood stream form G1


text: WTCMP

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Trypanosoma brucei brucei

text: Trypanosoma brucei brucei

text: Lister 427

text: Cell-cycle sorted T. brucei cells blood stream form G2/M


text: WTCMP

text: public

text: Trypanosoma brucei brucei

characteristic: organism

text: Trypanosoma brucei brucei

text: Lister 427

text: Cell-cycle sorted T. brucei cells blood stream form lateS

characteristic: title


text: WTCMP

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Trypanosoma brucei brucei

text: Trypanosoma brucei brucei

text: Lister 427

text: Cell-cycle sorted T. brucei cells procyclic form earlyS


text: WTCMP

text: public

text: Trypanosoma brucei brucei

text: Trypanosoma brucei brucei

text: Lister 427

text: Cell-cycle sorted T. brucei cells procyclic form G1


text: WTCMP

text: public

text: Trypanosoma brucei brucei

text: Trypanosoma brucei brucei

text: Lister 427

text: Cell-cycle sorted T. brucei cells procyclic form G2/M


text: WTCMP

text: public

text: Trypanosoma brucei brucei

text: Trypanosoma brucei brucei

text: Lister 427

text: Cell-cycle sorted T. brucei cells procyclic form lateS


text: WTCMP

text: public

text: promastigote

characteristic: cell type

text: Leishmania mexicana

text: Leishmania mexicana

text: L. mexicana M379 serial passage


text: UNIVERSITY OF CAMBRIDGE

text: public

tag: Namespace:UNIVERSITY OF CAMBRIDGE

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens


text: URMITE

text: public

text: Draft Genome Sequence of Clostridium septicum strain P1044 Isolated from a human stool in Marseille.

characteristic: description

text: Clostridium septicum

text: Clostridium septicum

text: Clostridium septicum genome


text: UNIVERSITY OF ILLINOIS CHAMPAIGN-URBANA

text: public

tag: Namespace:UNIVERSITY OF ILLINOIS CHAMPAIGN-URBANA

text: Fibroblast

text: pig

text: Primary Oncopig fibroblast cell line

text: Sus scrofa

text: Sus scrofa

text: Oncopig

text: Oncopig Fibroblast Cell Line


text: UNIVERSITY OF ILLINOIS CHAMPAIGN-URBANA

text: public

text: Fibroblast

text: pig

text: Primary Oncopig fibroblast cell line, treated with adenovirus encoding GFP.

text: Sus scrofa

text: Sus scrofa

text: Oncopig

text: Oncopig Fibroblast Cell Line


text: UNIVERSITY OF ILLINOIS CHAMPAIGN-URBANA

text: public

text: Fibroblast

text: pig

text: Primary Oncopig fibroblast cell line treated with adenovirus encoding Cre (AdCre) to produce an Oncopig STS cell lines.

text: Sus scrofa

text: Sus scrofa

text: Oncopig

text: Oncopig Fibroblast Cell Line


text: UNIVERSITY OF ILLINOIS CHAMPAIGN-URBANA

text: public

text: Fibroblast

text: pig

text: Primary Oncopig fibroblast cell line treated with adenovirus encoding Cre (AdCre) to produce an Oncopig STS cell lines. Maintained for 12 passages.

text: Sus scrofa

text: Sus scrofa

text: Oncopig

text: Oncopig Fibroblast Cell Line


text: UNIVERSITY OF ILLINOIS CHAMPAIGN-URBANA

text: public

text: Fibroblast

text: pig

text: Primary Oncopig fibroblast cell line treated with adenovirus encoding Cre (AdCre) to produce an Oncopig STS cell lines. Maintained for 99 passages.

text: Sus scrofa

text: Sus scrofa

text: Oncopig

text: Oncopig Fibroblast Cell Line


text: WTCMP

text: public

text: promastigote

text: MG

characteristic: location code

text: Leishmania chagasi

text: A

characteristic: sample group

characteristic: sample id

text: Leishmania chagasi

text: Leishmania L. chagasi sample 11-A


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: WTCMP

text: public

text: promastigote

text: MG

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 12-A


characteristic: External Id

text: WTCMP

characteristic: INSDC center name

text: public

text: promastigote

text: MG

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 13-A


text: WTCMP

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: promastigote

text: MG

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 14-A


text: WTCMP

text: public

characteristic: INSDC status

text: promastigote

text: MG

text: Leishmania chagasi

characteristic: organism

text: B

text: Leishmania chagasi

text: Leishmania L. chagasi sample 14-B


text: WTCMP

text: public

characteristic: SRA accession

text: promastigote

text: MA

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 01-A

characteristic: title


text: WTCMP

text: public

characteristic: Submitter Id

text: promastigote

characteristic: cell type

text: MA

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 02-A


text: WTCMP

text: public

text: promastigote

text: MA

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 03-A


text: WTCMP

text: public

text: promastigote

text: MA

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 04-A


text: WTCMP

text: public

text: promastigote

text: MA

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 05-A


text: WTCMP

text: public

text: promastigote

text: MA

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 07-A


text: WTCMP

text: public

text: promastigote

text: MG

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 15-A


text: WTCMP

text: public

text: promastigote

text: MG

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 16-A


text: WTCMP

text: public

text: promastigote

text: MG

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 17-A


text: WTCMP

text: public

text: promastigote

text: MG

text: Leishmania chagasi

text: B

text: Leishmania chagasi

text: Leishmania L. chagasi sample 17-B


text: WTCMP

text: public

text: promastigote

text: MG

text: Leishmania chagasi

text: C

text: Leishmania chagasi

text: Leishmania L. chagasi sample 17-C


text: WTCMP

text: public

text: promastigote

text: MG

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 18-A


text: WTCMP

text: public

text: promastigote

text: MG

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 19-A


text: WTCMP

text: public

text: promastigote

text: MG

text: Leishmania chagasi

text: B

text: Leishmania chagasi

text: Leishmania L. chagasi sample 19-B


text: WTCMP

text: public

text: promastigote

text: PI

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 01-A


text: WTCMP

text: public

text: promastigote

text: PI

text: Leishmania chagasi

text: B

text: Leishmania chagasi

text: Leishmania L. chagasi sample 01-B


text: WTCMP

text: public

text: promastigote

text: PI

text: Leishmania chagasi

text: C

text: Leishmania chagasi

text: Leishmania L. chagasi sample 01-C


text: WTCMP

text: public

text: promastigote

text: PI

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 02-A


text: WTCMP

text: public

text: promastigote

text: PI

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 03-A


text: WTCMP

text: public

text: promastigote

text: PI

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 04-A


text: WTCMP

text: public

text: promastigote

text: PI

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 05-A


text: WTCMP

text: public

text: promastigote

text: PI

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 07-A


text: WTCMP

text: public

text: promastigote

text: PI

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 08-A


text: WTCMP

text: public

text: promastigote

text: PI

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 09-A


text: WTCMP

text: public

text: promastigote

text: PI

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 10-A


text: WTCMP

text: public

text: promastigote

text: PI

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 11-A


text: WTCMP

text: public

text: promastigote

text: PI

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 12-A


text: WTCMP

text: public

text: promastigote

text: PP

text: Leishmania chagasi

text: A

text: Leishmania chagasi

text: Leishmania L. chagasi sample 75


text: PUBLIC HEALTH ENGLAND

text: public

tag: Namespace:PUBLIC HEALTH ENGLAND

characteristic: broker name

characteristic: description

text: Neisseria lactamica

text: Neisseria lactamica


text: PUBLIC HEALTH ENGLAND

text: public

text: Neisseria meningitidis

text: Neisseria meningitidis


text: PUBLIC HEALTH ENGLAND

text: public

text: Moraxella catarrhalis

text: Moraxella catarrhalis


text: PUBLIC HEALTH ENGLAND

text: public

text: Neisseria subflava

text: Neisseria subflava


text: PUBLIC HEALTH ENGLAND

text: public

text: Neisseria polysaccharea

text: Neisseria polysaccharea


text: PUBLIC HEALTH ENGLAND

text: public

text: unidentified

text: unidentified


text: PUBLIC HEALTH ENGLAND

text: public

text: Neisseria cinerea

text: Neisseria cinerea


text: PUBLIC HEALTH ENGLAND

text: public

text: Kingella denitrificans

text: Kingella denitrificans


text: Salmonella enterica

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: Salmonella enterica

characteristic: common name

text: Salmonella enterica

text: Salmonella enterica

characteristic: strain


text: Salmonella enterica

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: GBR

text: Salmonella enterica

text: Salmonella

characteristic: genus

characteristic: isolate

text: Salmonella enterica

text: Salmonella enterica

type: AMR curated data - CABBAGE

value: sulfisoxazole

value: mg/L

value: Salmonella enterica

value: trimethoprim-sulfamethoxazole

value: broth dilution

value: agar dilution

value: nalidixic acid

value: gentamicin

value: ampicillin

value: chloramphenicol

value: ciprofloxacin

value: trimethoprim

value: tetracycline


text: C.elegans

characteristic: ArrayExpress-Phenotype

text: Caenorhabditis elegans

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Caenorhabditis elegans

text: Caenorhabditis elegans

characteristic: sample description

text: Caenorhabditis elegans


text: Wild type

text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus

characteristic: title


characteristic: ENA-CHECKLIST

text: public

characteristic: collection date

text: human

characteristic: common name

text: the merged pair-ended reads from the metagenomic shotgun sequences of DNA isolated from virus-like particle from the human feces.

characteristic: description

text: ENVO:human-associated habitat

characteristic: environment (biome)

text: ENVO:human-associated habitat

characteristic: environment (feature)

text: ENVO:feces

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: Homo sapiens

characteristic: project name

text: Homo sapiens

text: Illumina

characteristic: sequencing method


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: UBERON:feces

characteristic: body habitat

text: UBERON:feces

characteristic: body product

text: UBERON:feces

characteristic: body site

characteristic: diabetes

text: true

characteristic: dol

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

characteristic: env feature

text: host-associated

characteristic: env package

text: feces

text: b

characteristic: experiment

text: USA:NY:NYC

characteristic: geo loc name

text: Mus musculus

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

characteristic: latitude

characteristic: longitude

text: mouse gut metagenome

text: NYUMC

text: true

text: stool

characteristic: sample type

text: mouse gut metagenome

text: female

characteristic: sex

text: Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in NOD mice

text: Control

characteristic: treatment

characteristic: week


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: UBERON:feces

characteristic: body habitat

text: UBERON:feces

characteristic: body product

text: UBERON:feces

characteristic: body site

characteristic: description

characteristic: diabetes

text: true

text: urban biome

text: animal-associated habitat

text: host-associated

text: feces

text: b

text: USA:NY:NYC

text: Mus musculus

text: mouse gut metagenome

characteristic: organism

text: NYUMC

text: true

text: stool

text: mouse gut metagenome

text: female

characteristic: title

text: Control


characteristic: ENA-CHECKLIST

text: UCSDMI

text: public

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: true

characteristic: dol

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

characteristic: env feature

text: host-associated

characteristic: env package

text: feces

text: b

characteristic: experiment

text: USA:NY:NYC

characteristic: geo loc name

text: Mus musculus

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

characteristic: latitude

characteristic: longitude

text: mouse gut metagenome

text: NYUMC

text: true

text: stool

characteristic: sample type

text: mouse gut metagenome

text: male

characteristic: sex

text: Control

characteristic: treatment

characteristic: week


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: UBERON:feces

characteristic: body habitat

text: UBERON:feces

characteristic: body product

text: UBERON:feces

characteristic: body site

characteristic: description

characteristic: diabetes

text: true

text: urban biome

text: animal-associated habitat

text: host-associated

text: feces

text: b

text: USA:NY:NYC

text: Mus musculus

text: mouse gut metagenome

characteristic: organism

text: NYUMC

text: true

text: stool

text: mouse gut metagenome

text: male

characteristic: title

text: Control


characteristic: ENA-CHECKLIST

text: UCSDMI

text: public

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: true

characteristic: dol

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

characteristic: env feature

text: host-associated

characteristic: env package

text: feces

text: b

characteristic: experiment

text: USA:NY:NYC

characteristic: geo loc name

text: Mus musculus

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

characteristic: latitude

characteristic: longitude

text: mouse gut metagenome

text: NYUMC

text: true

text: stool

characteristic: sample type

text: mouse gut metagenome

text: female

characteristic: sex

text: Control

characteristic: treatment

characteristic: week


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: UBERON:gastro-intestinal tract

characteristic: body habitat

text: UBERON:cecal mucosa

characteristic: body product

text: UBERON:cecum

characteristic: body site

characteristic: description

text: true

text: urban biome

text: animal-associated habitat

text: host-associated

text: organic material

text: b

text: USA:NY:NYC

text: Mus musculus

text: mouse gut metagenome

characteristic: organism

text: NYUMC

text: true

text: cecal content

text: mouse gut metagenome

text: female

characteristic: title

text: Control


text: UCSDMI

text: public

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: true

characteristic: dol

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

characteristic: env feature

text: host-associated

characteristic: env package

text: feces

text: b

characteristic: experiment

text: USA:NY:NYC

characteristic: geo loc name

text: Mus musculus

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

characteristic: latitude

characteristic: longitude

text: mouse gut metagenome

text: NYUMC

text: true

text: stool

characteristic: sample type

text: mouse gut metagenome

text: female

characteristic: sex

text: Control

characteristic: treatment

characteristic: week


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: UBERON:gastro-intestinal tract

characteristic: body habitat

text: UBERON:ileum mucosa

characteristic: body product

text: UBERON:ileum

characteristic: body site

characteristic: description

text: true

text: urban biome

text: animal-associated habitat

text: host-associated

text: organic material

text: b

text: USA:NY:NYC

text: Mus musculus

text: mouse gut metagenome

characteristic: organism

text: NYUMC

text: true

text: ileum content

text: mouse gut metagenome

text: female

characteristic: title

text: Control


text: UCSDMI

text: public

text: UBERON:gastro-intestinal tract

text: UBERON:cecal mucosa

text: UBERON:cecum

text: true

characteristic: dol

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

characteristic: env feature

text: host-associated

characteristic: env package

text: organic material

text: b

characteristic: experiment

text: USA:NY:NYC

characteristic: geo loc name

text: Mus musculus

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

characteristic: latitude

characteristic: longitude

text: mouse gut metagenome

text: NYUMC

text: true

text: cecal content

characteristic: sample type

text: mouse gut metagenome

text: female

characteristic: sex

text: Control

characteristic: treatment

characteristic: week


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: UBERON:gastro-intestinal tract

characteristic: body habitat

text: UBERON:ileum mucosa

characteristic: body product

text: UBERON:ileum

characteristic: body site

characteristic: description

text: true

text: urban biome

text: animal-associated habitat

text: host-associated

text: organic material

text: b

text: USA:NY:NYC

text: Mus musculus

text: mouse gut metagenome

characteristic: organism

text: NYUMC

text: true

text: ileum content

text: mouse gut metagenome

text: female

characteristic: title

text: Control


text: UCSDMI

text: public

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: true

characteristic: dol

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

characteristic: env feature

text: host-associated

characteristic: env package

text: feces

text: b

characteristic: experiment

text: USA:NY:NYC

characteristic: geo loc name

text: Mus musculus

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

characteristic: latitude

characteristic: longitude

text: mouse gut metagenome

text: NYUMC

text: true

text: stool

characteristic: sample type

text: mouse gut metagenome

text: male

characteristic: sex

text: Control

characteristic: treatment

characteristic: week


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: UBERON:gastro-intestinal tract

characteristic: body habitat

text: UBERON:cecal mucosa

characteristic: body product

text: UBERON:cecum

characteristic: body site

characteristic: description

text: true

text: urban biome

text: animal-associated habitat

text: host-associated

text: organic material

text: b

text: USA:NY:NYC

text: Mus musculus

text: mouse gut metagenome

characteristic: organism

text: NYUMC

text: true

text: cecal content

text: mouse gut metagenome

text: male

characteristic: title

text: Control


text: UCSDMI

text: public

text: UBERON:gastro-intestinal tract

text: UBERON:ileum mucosa

text: UBERON:ileum

text: true

characteristic: dol

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

characteristic: env feature

text: host-associated

characteristic: env package

text: organic material

text: b

characteristic: experiment

text: USA:NY:NYC

characteristic: geo loc name

text: Mus musculus

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

characteristic: latitude

characteristic: longitude

text: mouse gut metagenome

text: NYUMC

text: true

text: ileum content

characteristic: sample type

text: mouse gut metagenome

text: male

characteristic: sex

text: Control

characteristic: treatment

characteristic: week


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: UBERON:feces

characteristic: body habitat

text: UBERON:feces

characteristic: body product

text: UBERON:feces

characteristic: body site

characteristic: description

text: true

text: urban biome

text: animal-associated habitat

text: host-associated

text: feces

text: b

text: USA:NY:NYC

text: Mus musculus

text: mouse gut metagenome

characteristic: organism

text: NYUMC

text: true

text: stool

text: mouse gut metagenome

text: male

characteristic: title

text: Control


text: UCSDMI

text: public

text: UBERON:gastro-intestinal tract

text: UBERON:ileum mucosa

text: UBERON:ileum

text: true

characteristic: dol

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

characteristic: env feature

text: host-associated

characteristic: env package

text: organic material

text: b

characteristic: experiment

text: USA:NY:NYC

characteristic: geo loc name

text: Mus musculus

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

characteristic: latitude

characteristic: longitude

text: mouse gut metagenome

text: NYUMC

text: true

text: ileum content

characteristic: sample type

text: mouse gut metagenome

text: male

characteristic: sex

text: Control

characteristic: treatment

characteristic: week


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: UBERON:gastro-intestinal tract

characteristic: body habitat

text: UBERON:cecal mucosa

characteristic: body product

text: UBERON:cecum

characteristic: body site

characteristic: description

text: true

text: urban biome

text: animal-associated habitat

text: host-associated

text: organic material

text: b

text: USA:NY:NYC

text: Mus musculus

text: mouse gut metagenome

characteristic: organism

text: NYUMC

text: true

text: cecal content

text: mouse gut metagenome

text: male

characteristic: title

text: Control


text: UCSDMI

text: public

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

characteristic: diabetes

text: true

characteristic: dol

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

characteristic: env feature

text: host-associated

characteristic: env package

text: feces

text: b

characteristic: experiment

text: USA:NY:NYC

characteristic: geo loc name

text: Mus musculus

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

characteristic: latitude

characteristic: longitude

text: mouse gut metagenome

text: NYUMC

text: true

text: stool

characteristic: sample type

text: mouse gut metagenome

text: female

characteristic: sex

text: PAT

characteristic: treatment

characteristic: week


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: UBERON:feces

characteristic: body habitat

text: UBERON:feces

characteristic: body product

text: UBERON:feces

characteristic: body site

characteristic: description

characteristic: diabetes

text: true

text: urban biome

text: animal-associated habitat

text: host-associated

text: feces

text: b

text: USA:NY:NYC

text: Mus musculus

text: mouse gut metagenome

characteristic: organism

text: NYUMC

text: true

text: stool

text: mouse gut metagenome

text: female

characteristic: title

text: PAT


characteristic: ENA-CHECKLIST

text: UCSDMI

text: public

text: UBERON:feces

text: UBERON:feces

text: UBERON:feces

text: true

characteristic: dol

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

characteristic: env feature

text: host-associated

characteristic: env package

text: feces

text: b

characteristic: experiment

text: USA:NY:NYC

characteristic: geo loc name

text: Mus musculus

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

characteristic: latitude

characteristic: longitude

text: mouse gut metagenome

text: NYUMC

text: true

text: stool

characteristic: sample type

text: mouse gut metagenome

text: female

characteristic: sex

text: PAT

characteristic: treatment

characteristic: week


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: UBERON:gastro-intestinal tract

characteristic: body habitat

text: UBERON:cecal mucosa

characteristic: body product

text: UBERON:cecum

characteristic: body site

characteristic: description

text: true

text: urban biome

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