text: CEA, Evry

text: public

characteristic: SRA accession

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 MED5::3HA::HIS3 med17::KanMX6 // med17-98 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CEA, Evry

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:CEA, Evry

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: baker's yeast

characteristic: common name

text: Protocols: All strains were grown in YPD rich medium at 30 degrees C to 0.6 OD600, then shifted at 37 degrees C for 45min. The cultures were cross-linked with 1% formaldehyde for 10 min The cell pellets are resuspended in 1 ml of FA/SDS/PMSF buffer (50 mM HEPES-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X100, 0.1% sodium deoxycholate, 0.1% SDS, 1 mM PMSF) and transferred to 1.5 mL Eppendorf tubes. 0.75 mL glass beads (425-600 um, Sigma) are then added to each tube, and the yeast cells were lysed at 4 degrees C for 15 min by vortexing. Pierce the bottom of a 12 ml Greiner tube with a hot needle (0.7x30 mm or 0.5x15 mm) and place in a Falcon50 with a pierced cap. The lysates are transfered in the pierced tubes. Wash each Epp with twice 1 ml of FA/SDS/PMSF buffer (4 ml per extract). Spin down 1 min/2000 rpm. Gently resuspend the pellet with a 5 ml pipet and transfer in a sterile 15 ml Corex tube. Spin down 20 min / 12000 rpm / 4 degrees C in a JA17 rotor (Beckmann). Vacuum the supernatant. The cross-linked chromatin appears as a transparent layer around the pellet. Transfer the pellet in a 2 ml Epp with a burned Pasteur pipet. Add 0.8 ml of FA/SDS/PMSF buffer in the Corex and resuspend with the Pasteur pipet. Transfer in the Epp. Wash the Corex with 0.8 ml FA/SDS/PMSF buffer. Homogenize the Epp with the Pasteur pipet and ihncubate on a rotating wheal at 4 degrees C for 1 to 2 hours.Spin down 20 min / 12000 rpm / 4 degrees C. Vacuum the supernatant and resuspend in 1.6 ml FA/SDS/PMSF buffer with a burned Pasteur pipet.Place the tubes in a mix water / ice / NaCl. Sonicator settings: Pulse-60%-Power 4. Sonicate 3 times 40 sec with 20 sec intervals. Split in 200ul aliquots and performe an additional sonication step with Bioruptor (Diagenode), 6 cycles of 30s with medium intensity setting. Average size of fragments obtained is 200bp.Transfer in a 12 ml Greiner tube and add 0.5 ml FA/SDS/PMSF buffer. Incubate on a rotating wheal for 30 min to 1 hour at 4 degrees C. Spin down 30 min / 10000 rpm / 4 degrees C on a JA20 rotor (Beckmann).Transfer the supernatant in a new tube. Aliquot the supernatant (the chromatin is now soluble). Aliquots of 650 ul and freeze in liquid nitrogen.Chromatin fragment control: Take an aliquot of 100 ul of chromatin and add 25 ul Pronase buffer 5X and 6.25 ul of Pronase (20 mg/ml in H20). Incubate 1 hour at 37 degrees C and O/N at 65 degrees C (digestproteins and reverse crosslink). Add 3.5 ul of RNaseA 1mg/ml and incubate 1 hour at 37 degrees C. Purify on a Quiagen PCR purification column (Elute wih 50 ul Tris 10 mM pH8.5). Load on gel (1.5% in TAE-100V).Immunoprecipitation:Wash 50 ul of Dynabeads Ig 4 times with 500 ul PBS BSA 0.1% buffer. Resuspend in 100 ul PBS BSA 0.1 % buffer. Add antibody (5ul 8WG16 or 1ul 12CA5). Incubate 30 min at 1300 rpm in an Eppendorf shaker at 30 degrees C. Wash 2X 500 ul PBS BSA 0.1%. Wash 1X 500 ul PBS BSA 0.1% with shaking 10 min at 1300 rpm / 30 degrees C. Wash 1X 500 ul PBS BSA 0.1%.Spin down the chromatin from the -80 degrees C for 15 min / 12000 rpm / 4 degrees C. Add 50 ul of PBS BSA 10mg/ml to the beads and then 500 ul of chromatin.Incubate 2h at 21 degrees C in an Eppendorf shaker (1300 rpm). Resuspend with 500 ul FA/SDS and change tube. Wash 2X 1 ml FA/SDS + NaCl (final concentration 500 mM). Wash 1X 1 ml FA/SDS + NaCl with shaking 10 min at 1300 rpm / 21 degrees C. Wash 1X with 500 ul IP buffer (Tris pH7.5 125 mM, EDTA 25 mM, SDS 2.5%). Wash 1X with 500 ul TE. Elute with 125 ul Pronase Buffer 1X for 20 min at 65 degrees C in an Eppendorf shaker at 600 rpm. Cool down at RT. Add 6.25 ul Pronase to the supernatant. Incubate 1h at 37 degrees C and O/N at 65 degrees C. Add 25 ul of Pronase buffer 5X and 6.25 ul of Pronase to 100 ul of chromatin remaining from the initial tube (total DNA).Incubate 1h at 37 degrees C and O/N at 65 degrees C. Add 3.5 ul RNAseA (1mg/ml) and incubate 1h at 37 degrees C. Purify DNA on a Qiagen PCR purification column.

characteristic: description

text: tagging

characteristic: genetic modification

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 MED15::3HA::HIS3 med17::KanMX6 // med17-98 CEN TRP1

characteristic: genotype

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

characteristic: title

type: has member


text: CEA, Evry

text: public

characteristic: SRA accession

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 LEU2::3HA::SPT15 med17::KanMX6 // MED17 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


characteristic: ENA-CHECKLIST

text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 LEU2::3HA::SPT15 med17::KanMX6 // med17-98 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


characteristic: ENA-FIRST-PUBLIC

text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 LEU2::3HA::SPT15 med17::KanMX6 // med17-670 CEN TRP4

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


characteristic: ENA-LAST-UPDATE

text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 LEU2::3HA::SPT15 med17::KanMX6 // med17-670 CEN TRP3

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


characteristic: External Id

text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 KIN28::3HA::HIS3 med17::KanMX6 // MED17 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

characteristic: INSDC center name

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 deltamed17::KanMX6 / MED17 CEN TRP1 MED5::3HA::HIS3

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

characteristic: INSDC first public

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 KIN28::3HA::HIS3 med17::KanMX6 // med17-98 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

characteristic: INSDC last update

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 MED15::3HA::HIS3 med17::KanMX6 // med17-444 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

text: public

characteristic: INSDC status

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 RAD3::3HA::HIS3 med17::KanMX6 // MED17 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

text: public

characteristic: Submitter Id

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 MED5::3HA::HIS3 med17::KanMX6 // med17-504 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

text: public

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 RAD3::3HA::HIS3 med17::KanMX6 // med17-98 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

characteristic: common name

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 deltamed17::KanMX6 / MED17 CEN TRP1 MED15::3HA::HIS3

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

characteristic: description

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 MED5::3HA::HIS3 med17::KanMX6 // med17-444 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

characteristic: genetic modification

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 MED5::3HA::HIS3 med17::KanMX6 // MED17 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 MED15::3HA::HIS3 med17::KanMX6 // med17-670 CEN TRP1

characteristic: genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

text: Protocols: All strains were grown in YPD rich medium at 30 degrees C to 0.6 OD600, then shifted at 37 degrees C for 45min. The cultures were cross-linked with 1% formaldehyde for 10 min The cell pellets are resuspended in 1 ml of FA/SDS/PMSF buffer (50 mM HEPES-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X100, 0.1% sodium deoxycholate, 0.1% SDS, 1 mM PMSF) and transferred to 1.5 mL Eppendorf tubes. 0.75 mL glass beads (425-600 um, Sigma) are then added to each tube, and the yeast cells were lysed at 4 degrees C for 15 min by vortexing. Pierce the bottom of a 12 ml Greiner tube with a hot needle (0.7x30 mm or 0.5x15 mm) and place in a Falcon50 with a pierced cap. The lysates are transfered in the pierced tubes. Wash each Epp with twice 1 ml of FA/SDS/PMSF buffer (4 ml per extract). Spin down 1 min/2000 rpm. Gently resuspend the pellet with a 5 ml pipet and transfer in a sterile 15 ml Corex tube. Spin down 20 min / 12000 rpm / 4 degrees C in a JA17 rotor (Beckmann). Vacuum the supernatant. The cross-linked chromatin appears as a transparent layer around the pellet. Transfer the pellet in a 2 ml Epp with a burned Pasteur pipet. Add 0.8 ml of FA/SDS/PMSF buffer in the Corex and resuspend with the Pasteur pipet. Transfer in the Epp. Wash the Corex with 0.8 ml FA/SDS/PMSF buffer. Homogenize the Epp with the Pasteur pipet and ihncubate on a rotating wheal at 4 degrees C for 1 to 2 hours.Spin down 20 min / 12000 rpm / 4 degrees C. Vacuum the supernatant and resuspend in 1.6 ml FA/SDS/PMSF buffer with a burned Pasteur pipet.Place the tubes in a mix water / ice / NaCl. Sonicator settings: Pulse-60%-Power 4. Sonicate 3 times 40 sec with 20 sec intervals. Split in 200ul aliquots and performe an additional sonication step with Bioruptor (Diagenode), 6 cycles of 30s with medium intensity setting. Average size of fragments obtained is 200bp.Transfer in a 12 ml Greiner tube and add 0.5 ml FA/SDS/PMSF buffer. Incubate on a rotating wheal for 30 min to 1 hour at 4 degrees C. Spin down 30 min / 10000 rpm / 4 degrees C on a JA20 rotor (Beckmann).Transfer the supernatant in a new tube. Aliquot the supernatant (the chromatin is now soluble). Aliquots of 650 ul and freeze in liquid nitrogen.Chromatin fragment control: Take an aliquot of 100 ul of chromatin and add 25 ul Pronase buffer 5X and 6.25 ul of Pronase (20 mg/ml in H20). Incubate 1 hour at 37 degrees C and O/N at 65 degrees C (digestproteins and reverse crosslink). Add 3.5 ul of RNaseA 1mg/ml and incubate 1 hour at 37 degrees C. Purify on a Quiagen PCR purification column (Elute wih 50 ul Tris 10 mM pH8.5). Load on gel (1.5% in TAE-100V).Immunoprecipitation:Wash 50 ul of Dynabeads Ig 4 times with 500 ul PBS BSA 0.1% buffer. Resuspend in 100 ul PBS BSA 0.1 % buffer. Add antibody (5ul 8WG16 or 1ul 12CA5). Incubate 30 min at 1300 rpm in an Eppendorf shaker at 30 degrees C. Wash 2X 500 ul PBS BSA 0.1%. Wash 1X 500 ul PBS BSA 0.1% with shaking 10 min at 1300 rpm / 30 degrees C. Wash 1X 500 ul PBS BSA 0.1%.Spin down the chromatin from the -80 degrees C for 15 min / 12000 rpm / 4 degrees C. Add 50 ul of PBS BSA 10mg/ml to the beads and then 500 ul of chromatin.Incubate 2h at 21 degrees C in an Eppendorf shaker (1300 rpm). Resuspend with 500 ul FA/SDS and change tube. Wash 2X 1 ml FA/SDS + NaCl (final concentration 500 mM). Wash 1X 1 ml FA/SDS + NaCl with shaking 10 min at 1300 rpm / 21 degrees C. Wash 1X with 500 ul IP buffer (Tris pH7.5 125 mM, EDTA 25 mM, SDS 2.5%). Wash 1X with 500 ul TE. Elute with 125 ul Pronase Buffer 1X for 20 min at 65 degrees C in an Eppendorf shaker at 600 rpm. Cool down at RT. Add 6.25 ul Pronase to the supernatant. Incubate 1h at 37 degrees C and O/N at 65 degrees C. Add 25 ul of Pronase buffer 5X and 6.25 ul of Pronase to 100 ul of chromatin remaining from the initial tube (total DNA).Incubate 1h at 37 degrees C and O/N at 65 degrees C. Add 3.5 ul RNAseA (1mg/ml) and incubate 1h at 37 degrees C. Purify DNA on a Qiagen PCR purification column.

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 RAD3::3HA::HIS3 med17::KanMX6 // med17-670 CEN TRP1

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 MED5::3HA::HIS3 med17::KanMX6 // med17-98 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

characteristic: title


text: CEA, Evry

text: public

characteristic: SRA accession

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 RAD3::3HA::HIS3 med17::KanMX6 // med17-504 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


characteristic: ENA-CHECKLIST

text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 KIN28::3HA::HIS3 med17::KanMX6 // med17-504 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


characteristic: ENA-FIRST-PUBLIC

text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 MED5::3HA::HIS3 med17::KanMX6 // med17-670 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


characteristic: ENA-LAST-UPDATE

text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 RAD3::3HA::HIS3 med17::KanMX6 // med17-444 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


characteristic: External Id

text: CEA, Evry

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-delta200 ade2-101uaa trp1-delta63 lys2-801uag leu2-delta1 MED15::3HA::HIS3 med17::KanMX6 // med17-504 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


characteristic: INSDC center name

text: public

tag: Namespace:Institute for Molecular Biology and Tumor Research

text: ArrayExpress

text: mouse embryonic fibroblast cell

characteristic: cell type

text: house mouse

text: Protocols: MEFs were kept in DMEM/Hams F-10 (1:1) (PAA/GE Healthcare) supplemented with 10% FCS (Fetal Bovine Serum Gold, PAA), 1% PenStrep (Sigma). DNA was immunoprecipitated using the respective antibody in accordance to the One-Day Chip kit (Diagenode) protocol. Four individual ChIPs were pooled and precipitated DNA was purified using Qiaquick columns (Qiagen). Five nanogram of precipitated DNA was used for library preparation using the Microplex libary preparation kit.

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: Institute for Molecular Biology and Tumor Research

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: mouse embryonic fibroblast cell

text: house mouse

text: deletion

text: delta Sp2

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: ArrayExpress

characteristic: broker name

text: mouse embryonic fibroblast cell

text: house mouse

characteristic: common name

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: ArrayExpress

text: mouse embryonic fibroblast cell

text: house mouse

characteristic: description

text: deletion

characteristic: genetic modification

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: ArrayExpress

text: mouse embryonic fibroblast cell

text: house mouse

text: deletion Sp2

text: wild type genotype

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus


text: public

characteristic: SRA accession

text: ArrayExpress

text: mouse embryonic fibroblast cell

text: house mouse

text: deletion

text: delta Sp3

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: European Molecular Biology Laboratory

text: public

tag: Namespace:European Molecular Biology Laboratory

text: ArrayExpress

text: house mouse

text: Protocols: Mouse strains were intercrosses between Pdgfra::GFP (Hamilton et al. Mol Cell Biol. 23:4013-4025) and strain 129 estrous-checked females. Embryos were collected from the oviduct or uterus in M2 medium (Sigma) at progressive developmental stages between E2.5 and E5.5. Embryonic diapause was induced by surgical removal of both ovaries from female mice on the morning of the third day of pregnancy (E2.5) and embryos were flushed at E6.5. For morula and early blastocyst stages zona pellucidae were removed using acid Tyrode’s solution (Sigma). Blastocysts from E3.25-4.5 were subjected to immunosurgery as previously described (Solter and Knowles, Proc Natl Acad Sci USA 72:5099-102; Nichols et al. Cell 95:379-91). Briefly, blastocysts were incubated for 15min in a 1:5 dilution of anti-mouse rabbit serum (Sigma) in N2B27 medium, washed in N2B27 and further incubated for 15min in a 1:5 dilution of rat serum (in-house) in N2B27 for the complement reaction. Embryos were transferred into N2B27 without washing and incubated for 15min to allow efficient cell lysis. The ICM was subsequently dissociated from residual trophectoderm with a narrowly fitting glass pipette. For postimplantation embryos the epiblast was isolated by manual dissection. Extraembryonic ectoderm was first removed with a wide mouth-controlled pipette, and the visceral endoderm was then mechanically separated by drawing the embryonic portion through a narrow glass aperture. Dissociation of morulae, ICMs and postimplantation epiblast was performed in a 1:1 mixture of 0.025% trypsin plus EDTA (Invitrogen) and 0.025% trypsin (Invitrogen) plus 1% chick serum (Sigma). Morulae and early ICMs were incubated for 5min at 37 C, and E4.5 ICMs and postimplantation epiblasts were incubated for 10min. The explants were washed in N2B27 supplemented with 10µM HEPES and 1.5mg/ml BSA (Gibco) and dissociated in a small drop of medium using blunted microcapillaries with an inner diameter large enough to accommodate approximately 2-3 cells. Cells of the primitive endoderm lineage were distinguished from epiblast cells by Pdgfra::GFP fluorescence and manually sorted under a dissection microscope. Mouse ES cells were dissociated by conventional methods in bulk culture; single-cell suspensions were prepared and 20 cells were manually selected with a blunted microcapillary for further processing. Cells were transferred immediately into 4.5ul of single-cell lysis buffer and snap frozen on dry ice. cDNA synthesis was performed using whole transcriptome preamplification (Tang et al. Nat Methods 6:377-382, Tang et al. Nat Protoc. 5:516-535). cDNA was preamplified for 20 cycles using a single-temperature protocol in a Veriti 96 Well Thermal Cycler (Applied Biosystems). Preamplified cDNA samples were sheared by ultrasonication on a Covaris S2 for 80s with the following parameter settings: Duty Cycle = 10, Cycles per Burst = 200, Intensity = 4. Samples were ethanol precipitated and resuspended in Tris buffer for subsequent enzymatic modifications. End repair was carried out with T4 DNA polymerase and T4 polynucleotide kinase (New England Biolabs) and samples were purified with Ampure XP paramagnetic beads (Beckman Coulter). Blunt-end, 3'-phosphorylated products were 3'-adenylated with exo- Klenow fragment in the presence of dATPs (New England Biolabs), purified with Ampure beads and ligated to sequencing adapters (Illumina) by T4 DNA ligase at 20 C for 30 minutes. PCR amplification of library constructs was carried out with AccuPrime DNA polymerase (Invitrogen) for 13 cycles on a Bio-Rad C1000 thermocycler using denaturing and annealing conditions optimized for even A/T vs. G/C processing (Aird et al. Genome Biol 12:R18). Molarity and size distribution of sequencing libraries were assessed by DNA 1000 microfluidic chips on the 2100 Bioanalyzer (Agilent).

text: early blastocyst

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: inner cell mass

characteristic: organism part

text: Mus musculus

text: 129S4 Pdgfra::GFP

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: European Molecular Biology Laboratory

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: house mouse

text: expanded blastocyst

text: Mus musculus

text: Mus musculus

text: primitive endoderm

text: Mus musculus

text: 129S4 Pdgfra::GFP


text: European Molecular Biology Laboratory

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

text: postimplantation blastocyst

text: Mus musculus

text: Mus musculus

text: postimplantation epiblast

text: Mus musculus

text: 129S4 Pdgfra::GFP


text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: embryonic stem cells

text: Mus musculus

text: Mus musculus

text: cell line (in vitro cultured)

text: Mus musculus


text: European Molecular Biology Laboratory

text: public

characteristic: SRA accession

text: ArrayExpress

text: house mouse

text: expanded blastocyst

text: Mus musculus

characteristic: organism

text: Mus musculus

text: preimplantation epiblast

text: Mus musculus

text: 129S4 Pdgfra::GFP


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: house mouse

text: cleavage 8-cell

text: Mus musculus

text: Mus musculus

text: morula

text: Mus musculus

text: 129S4 Pdgfra::GFP

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: house mouse

text: embryonic diapause

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: preimplantation epiblast

text: Mus musculus

text: 129S4 Pdgfra::GFP


text: 8.6 weeks

characteristic: ArrayExpress-Age

text: WT

characteristic: ArrayExpress-Genotype

text: Lin- bone marrow cells

characteristic: ArrayExpress-OrganismPart

text: female

characteristic: ArrayExpress-Sex

text: Mus Musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: house mouse

text: Mus musculus

text: Lin- bone marrow cells

characteristic: sample description

text: Mus musculus


text: 8.6 weeks

text: KO

text: Lin- bone marrow cells

text: female

text: Mus Musculus

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: Lin- bone marrow cells

text: Mus musculus


text: 12.2 weeks

text: WT

text: Lin- bone marrow cells

text: female

text: Mus Musculus

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Lin- bone marrow cells

text: Mus musculus


text: 12.2 weeks

text: KO

text: Lin- bone marrow cells

text: female

text: Mus Musculus

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

text: Mus musculus

text: Lin- bone marrow cells

text: Mus musculus


text: Gallus gallus

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: chicken

text: Gallus gallus

text: Gallus gallus

characteristic: strain


text: public

text: E-MTAB-2972:Deckers_lab_Sep2014_NFkB_HKL_IFNb

tag: Namespace:Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna

text: ArrayExpress

characteristic: broker name

text: bone marrow macrophage

characteristic: cell type

text: house mouse

text: Protocols: Bone marrow-derived macrophages (BMDM) were obtained by culture of mouse bone marrow in DMEM +10%FCS +10% L-cell-derived conditioned medium containing colony-stimulating factor 1. After 10 days the cells were used for experiment. 2.5x107 cells were seeded on a 15cm dish and treated as follows. Cells used for ChIPseq experiments with antibodies against STAT1 were treated with 250U/ml IFNb for 2 hours. Cells subjected to ChIP with antibodies against NFkB p65 or RNA polymerase II were treated with IFNb (250U/ml) and hkL (equivalent to MOI 50) for 4 hours. After treatment formaldehyde was added to the cells to a final concentration of 1% and dishes were incubated for 10 minutes at 37C. The reaction was quenched by adding 2.5 M glycine to a final concentration of 125 mM for 10 minutes. The fixed cells were washed with PBS and scraped. After centrifugation for 10 minutes at 600g cells were washed with wash I (0.25%Triton X-100; 0.01M EDTA; 0.5mM EGTA; 0.01M Hepes) for 10 minutes at 4C, followed by another centrifugation step. The pellet was resuspended in wash II (0.2M NaCl; 1mM EDTA; 0.5mM EGTA; 0.01M Hepes) and kept for 10 minutes at 4C. Cells were lysed over night with lysis buffer (1% SDS; 0.05M Tris pH 8; 0.01M EDTA) at 4C. The cells were then sonicated 27 x 30 seconds using a Bioruptor sonicator. This resulted in chromatin fragments with an average length of 300 bp. Samples were centrifuged twice at 16.000g for 15 min and the supernatant was used for the subsequent steps. 5 ug antibody was added to the chromatin and rotated overnight at 4C. Protein G Dynabeads (Invitrogen) were blocked over night in 0.1% BSA and on the next day added to the chromatin/antibody mixture and incuabted for 3 hours at 4C. Beads were then washed five times for 10 minutes in RIPA buffer (0.15M NaCl; 0.05M Tris pH 8; 0.1% SDS; 0.5% NaDoc; 1% NP40), once in high salt buffer (0.5M NaCl; 0.05M Tris pH 8; 0.1% SDS; 1% NP40), once in LiCl buffer (0.25M LiCl; 0.05M Tris pH 8; 0.5% NaDoc; 1% NP40), and two times in TE buffer. Beads were then shaken in elution buffer at room temperature for 40 minutes and 20ul 4M NaCl was added to the eluted sample. Samples were incubated at 65C overnight to reverse the cross-links. Samples were then treated with proteinase K (2ul ptroteinase K, 8ul EDTA 0.5M pH 7.5 and16ul IM TRIS pH 6.5) for 60 min at 55C. 500ul Phenol/Chloroform/Isoamyl alcohol (25/24/1) was added to all samples and they were then centrifuged for 5 minutes at 16000g. The upper phase was used for DNA precipitation. 5-10 ng of DNA precipitate was used for the generation of sequencing libraries using the KAPA library preparation kit for Illumina systems. Libraries were quantified with a Bioanalyzer dsDNA 1000 assay kit (Agilent) and a QPCR NGS library quantification kit (KAPA).

characteristic: description

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: female

characteristic: sex

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-2972:Deckers_lab_Sep2014_STAT1_untreated

text: ArrayExpress

text: bone marrow macrophage

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: female


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-2972:Deckers_lab_Sep2014_STAT1_IFNb

characteristic: Submitter Id

text: ArrayExpress

text: bone marrow macrophage

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-2972:Deckers_lab_Sep2014_NFkB_untreated

text: ArrayExpress

text: bone marrow macrophage

text: house mouse

characteristic: common name

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: female


text: public

text: E-MTAB-2972:Deckers_lab_Sep2014_Pol2_untreated

text: ArrayExpress

characteristic: broker name

text: bone marrow macrophage

characteristic: cell type

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: female


text: public

text: E-MTAB-2972:Deckers_lab_Sep2014_Pol2_HKL_IFNb

text: ArrayExpress

text: bone marrow macrophage

text: house mouse

characteristic: description

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: female


text: public

text: E-MTAB-2972:Deckers_lab_Sep2014_Pol2_IFNb

text: ArrayExpress

text: bone marrow macrophage

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: female

characteristic: sex

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-2972:Deckers_lab_Sep2014_Pol2_HKL

text: ArrayExpress

text: bone marrow macrophage

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: female


text: male

characteristic: ArrayExpress-Sex

text: Mus Musculus

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: house mouse

text: Mus musculus

text: ESC

characteristic: sample description

text: Mus musculus


text: Mus Musculus

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Control

text: Mus musculus


E-MTAB-2974:Adult Cell 3

characteristic: ENA-FIRST-PUBLIC

text: Ruhr University Bochum

text: public

text: E-MTAB-2974:Adult Cell 3

tag: Namespace:Ruhr University Bochum

text: ArrayExpress

characteristic: broker name

text: olfactory sensory neuron

characteristic: cell type

text: house mouse

characteristic: common name

text: Protocols: cDNA was extracted and generated using the SeqPlex RNA Amplification Kit from Sigma For library preparation we used the Illumina Nextera XT DNA sample preparation protocol (Part # 15031942 Rev. C) starting with an input amount of 1 ng amplicon DNA.

text: adult

characteristic: developmental stage

text: mOR-EG GFP

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Adult Cell 3


E-MTAB-2974:P-0 Cell 3

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Ruhr University Bochum

text: public

text: E-MTAB-2974:P-0 Cell 3

text: ArrayExpress

text: olfactory sensory neuron

text: house mouse

characteristic: description

text: mOR-EG GFP

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: P-0 Cell 3

characteristic: title


E-MTAB-2974:P-10 Cell 1

text: Ruhr University Bochum

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-2974:P-10 Cell 1

text: ArrayExpress

text: olfactory sensory neuron

text: house mouse

text: mOR-EG GFP

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: P-10 Cell 1


E-MTAB-2974:Adult Cell 4

characteristic: ENA-CHECKLIST

text: Ruhr University Bochum

characteristic: INSDC last update

text: public

text: E-MTAB-2974:Adult Cell 4

text: ArrayExpress

text: olfactory sensory neuron

text: house mouse

text: adult

text: mOR-EG GFP

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Adult Cell 4


E-MTAB-2974:P-4 Cell 4

text: Ruhr University Bochum

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-2974:P-4 Cell 4

text: ArrayExpress

text: olfactory sensory neuron

text: house mouse

text: mOR-EG GFP

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: P-4 Cell 4


E-MTAB-2974:P-10 Cell 2

characteristic: ENA-FIRST-PUBLIC

text: Ruhr University Bochum

text: public

text: E-MTAB-2974:P-10 Cell 2

characteristic: Submitter Id

text: ArrayExpress

text: olfactory sensory neuron

text: house mouse

text: mOR-EG GFP

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: P-10 Cell 2


E-MTAB-2974:P-0 Cell 4

text: Ruhr University Bochum

text: public

text: E-MTAB-2974:P-0 Cell 4

text: ArrayExpress

characteristic: broker name

text: olfactory sensory neuron

characteristic: cell type

text: house mouse

text: mOR-EG GFP

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: P-0 Cell 4


E-MTAB-2974:P-10 Cell 3

text: Ruhr University Bochum

text: public

text: E-MTAB-2974:P-10 Cell 3

text: ArrayExpress

text: olfactory sensory neuron

text: house mouse

characteristic: common name

characteristic: developmental stage

text: mOR-EG GFP

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: P-10 Cell 3


E-MTAB-2974:P-4 Cell 2

characteristic: ENA-LAST-UPDATE

text: Ruhr University Bochum

text: public

text: E-MTAB-2974:P-4 Cell 2

text: ArrayExpress

text: olfactory sensory neuron

text: house mouse

text: mOR-EG GFP

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: P-4 Cell 2


E-MTAB-2974:Adult Cell 2

characteristic: External Id

text: Ruhr University Bochum

text: public

text: E-MTAB-2974:Adult Cell 2

text: ArrayExpress

text: olfactory sensory neuron

text: house mouse

characteristic: description

text: adult

text: mOR-EG GFP

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Adult Cell 2


E-MTAB-2974:P-0 Cell 1

text: Ruhr University Bochum

text: public

text: E-MTAB-2974:P-0 Cell 1

text: ArrayExpress

text: olfactory sensory neuron

text: house mouse

text: mOR-EG GFP

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: P-0 Cell 1

characteristic: title


E-MTAB-2974:Adult Cell 1

text: Ruhr University Bochum

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-2974:Adult Cell 1

text: ArrayExpress

text: olfactory sensory neuron

text: house mouse

text: adult

text: mOR-EG GFP

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Adult Cell 1


E-MTAB-2974:P-4 Cell 3

characteristic: ENA-CHECKLIST

text: Ruhr University Bochum

characteristic: INSDC last update

text: public

text: E-MTAB-2974:P-4 Cell 3

text: ArrayExpress

text: olfactory sensory neuron

text: house mouse

text: mOR-EG GFP

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: P-4 Cell 3


E-MTAB-2974:P-0 Cell 2

text: Ruhr University Bochum

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-2974:P-0 Cell 2

text: ArrayExpress

text: olfactory sensory neuron

text: house mouse

text: mOR-EG GFP

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: P-0 Cell 2


E-MTAB-2974:P-10 Cell 4

characteristic: ENA-FIRST-PUBLIC

text: Ruhr University Bochum

text: public

text: E-MTAB-2974:P-10 Cell 4

characteristic: Submitter Id

text: ArrayExpress

text: olfactory sensory neuron

text: house mouse

text: mOR-EG GFP

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: P-10 Cell 4


E-MTAB-2974:P-4 Cell 1

text: Ruhr University Bochum

text: public

text: E-MTAB-2974:P-4 Cell 1

text: ArrayExpress

characteristic: broker name

text: olfactory sensory neuron

characteristic: cell type

text: house mouse

text: mOR-EG GFP

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: P-4 Cell 1


text: public

tag: Namespace:Department of Cell and Molecular Biology, Karolinska Institutet

text: ArrayExpress

text: human

characteristic: common name

text: DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. Protocols: Single cells (n = 41) were randomly picked by mouth pipetting with a finely pulled glass capillary and placed directly into lysis buffer containing 1 uL of RNase inhibitor and 19 uL of 0.2% (vol/vol) Triton X-100 solution (Sigma-Aldrich, Germany). The 8-strip PCR tubes containing cells were immediately frozen on dry ice and kept at -80C for downstream applications. Regarding spike-ins: 0.1uL of a 4*10^-6 dilution of the ERCC RNA spike-in mix 1 (Ambion) was added to each sample. Picelli et al, Full-length RNA-seq from single cells using Smart-seq2, Nature Protocols, 2014

text: adult

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: animal ovary

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex

text: OK

characteristic: single cell well quality


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Cell and Molecular Biology, Karolinska Institutet

text: public

text: ArrayExpress

text: human

characteristic: description

text: adult

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: animal ovary

text: Homo sapiens

text: female

text: OK

characteristic: title


text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: Mus musculus


text: Danio rerio

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: Danio rerio


text: ESC

characteristic: ArrayExpress-CellType

text: undifferentiated

characteristic: ArrayExpress-DevelopmentalStage

text: primed

characteristic: ArrayExpress-GrowthCondition

text: female

text: Homo sapiens

text: SC

text: public

text: human

text: Homo sapiens

text: ESC

characteristic: sample description

text: Homo sapiens


text: ESC

text: undifferentiated

text: primed

text: male

text: Mus musculus

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: house mouse

text: Mus musculus

characteristic: organism

text: ESC

text: Mus musculus


text: public

tag: Namespace:European Molecular Biology Laboratory - European Bioinformatics Institute

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: BALB/c CD4+CD25- T cells were isolated by negatively depleting splenocytes stained with FITC-conjugated depletion cocktail antibodies including anti-CD8, anti-CD19, anti-CD11b, anti-CD11c, anti-Ly6G, anti-TER119 and anti-CD25 using autoMACS machine (Miltenyi Biotc). Isolated mouse primary T cells were cultured in RPMI-1640 medium supplemented with 10% FCS, antibiotics and 50uM 2-mercaptoethanol. Primary T cells were transduced with virus carrying Foxp3 and its mutants. Transduced cells were allowed to rest for 48 h in RPMI medium with IL2. The resting cell expressing transduction marker rCD8a were sorted by FACS or autoMACS. For re-activation sample, sorted cells were activated with plate-coated anti-CD3 (5 ug/ml), soluble anti-CD28 (1 ug/ml) for 8 h. mRNA isolation was performed using uMACS mRNA isolation kit (Miltenyi Biotec). 5x106 cells of each sample were lysed for mRNA isolation. cDNA synthesis was performed using the uMACS cDNA synthesis module (Miltenyi Biotec). Second strand was synthesized using E.coli DNA polymerase I (NEB), E.coli DNA ligase (NEB) and E.coli RNaseH (NEB) in second strand synthesis buffer (Invitrogen) at 16C for 2.5 h. Double strand DNA was fragmented by sonication using Bioruptor UCD-400 (Diagenode), with 20 cycles of (30 sec On; 30 second off). Fragmented samples were end-repaired using Klenow large fragment (NEB), T4 DNA polymerase(NEB) and T4 polynucleotide kinase (NEB) at 20C for 30 min. Purified blunt-ended DNA was 3' adenylated using 3' greater than 5' exo- Klenow fragment (NEB) at 37C for 30 min. After purification, adapters containing 6 bp barcodes from sample prep oligonucleotide kit (Illumina) were ligated to 3' A-tailed DNA fragment at 20C for 30 min using T4 DNA ligase (NEB). Each DNA sample was amplified via 18-cycle PCR using universal primers from the sample prep oligonucleotide kit. The amplified library was size-selected from 200-400 bps using 2% agarose gel and quantified with a high-sensitivity DNA chip (Agilent) using agilent bioanalyzer.

characteristic: description

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: title

text: Foxp3 delta-m4.2

characteristic: transduced gene


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory - European Bioinformatics Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: GFP negative control


characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Foxp3 delta-ProR


text: public

text: ArrayExpress

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Foxp3 delta-m4.2


text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Foxp3 delta-exon1


text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Wild-type Foxp3


text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Foxp3 delta-FKH


text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Foxp3 delta-FKHnls


text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Foxp3 delta-m5


text: Danio rerio

characteristic: ArrayExpress-Species

text: TL/AB

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

text: Danio rerio

text: Exome

characteristic: sample description

text: Danio rerio

text: TL/AB

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: KI-BN

text: public

text: fruit fly

text: HT-SELEX generated data with following information on the name of the entry (Separated with underscores):Batch_BarcodeDesign_SelectionCycle

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: BtbVII


text: KI-BN

text: public

text: fruit fly

characteristic: description

text: Drosophila melanogaster

text: Drosophila melanogaster

text: rib

characteristic: title


characteristic: ENA-CHECKLIST

text: KI-BN

characteristic: INSDC center name

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster


text: KI-BN

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: prd


characteristic: ENA-FIRST-PUBLIC

text: KI-BN

text: public

characteristic: INSDC status

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: HGTX


text: KI-BN

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: usp


text: KI-BN

text: public

text: fruit fly

characteristic: common name

text: Drosophila melanogaster

text: Drosophila melanogaster

text: grn


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Oli


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: ey


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: GATAe


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Rx


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: repo


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: bsh


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Max


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: crp


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Jra


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: kay


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: toe


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: crc


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: cad


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: croc


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: bs


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: ems


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: gsb


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: HLHmdelta


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: bap


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: bcd


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: bigmax


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: HLHmgamma


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: ac


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Dll


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: eyg


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: fkh


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: ftz


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: lab


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: nau


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: odd


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: pnr


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Poxm


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

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text: fruit fly

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text: SC

text: public

text: house mouse

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text: SC

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text: malaria parasite P. vivax

text: Plasmodium vivax

text: Plasmodium vivax


text: The Roslin Institute

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tag: Namespace:The Roslin Institute

text: ArrayExpress

characteristic: broker name

text: heterophil

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text: chicken

text: Protocols: Macrophages and dendritic cells were cultured from bone marrow by standard methods (Garceau et al. 2010 and Wu et al. 2010, respectively), and heterophils isolated from blood by standard methods (Kogut et al. 1995). Cells were cultured with or without LPS for 24 h before RNA was isolated Standard Trizol extraction method Samples were prepared for mRNA sequencing using 2ug of total RNA starting material following the Illumina TruSeq RNA Sample Preparation v2 kit protocol.

characteristic: description

text: Gallus gallus

characteristic: organism

text: Gallus gallus

text: Gallus gallus


characteristic: ENA-CHECKLIST

text: The Roslin Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: macrophage

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text: Gallus gallus

text: Gallus gallus

text: Gallus gallus

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: The Roslin Institute

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text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: dendritic cell

text: chicken

text: Gallus gallus

text: Gallus gallus

text: Gallus gallus


text: Gallus gallus

text: SC

text: public

characteristic: Submitter Id

text: chicken

characteristic: common name

text: Gallus gallus

text: Gallus gallus

characteristic: strain


text: Danio rerio

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characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: Danio rerio


E-MTAB-2999:Notch1-2-KO 2

characteristic: External Id

text: Sanquin Blood Supply

text: public

text: E-MTAB-2999:Notch1-2-KO 2

tag: Namespace:Sanquin Blood Supply

text: ArrayExpress

characteristic: broker name

text: H-2 Db-NP366-374+ CD8+ T cell

text: house mouse

text: Protocols: Total RNA was extracted with TRIzol reagent (Invitrogen) according to the manufacturers protocol. Total RNA was further purified by nucleospin RNAII columns (Macherey-Nagel). RNA was amplified using the Superscript RNA amplification system (Invitrogen) and labeled with the ULS system (Kraetech), using either Cy3 or Cy5 dyes (Amersham).

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Notch1-2-KO 2


E-MTAB-2999:MPC 2

text: Sanquin Blood Supply

text: public

text: E-MTAB-2999:MPC 2

text: ArrayExpress

text: CD127+ KLRG1- H-2 Db-NP366-374+ CD8+ T cell

characteristic: cell type

text: house mouse

characteristic: description

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: MPC 2


E-MTAB-2999:Notch1-2-KO 3

characteristic: ENA-CHECKLIST

text: Sanquin Blood Supply

text: public

text: E-MTAB-2999:Notch1-2-KO 3

text: ArrayExpress

text: H-2 Db-NP366-374+ CD8+ T cell

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Notch1-2-KO 3


E-MTAB-2999:Notch1-2-WT 2

text: Sanquin Blood Supply

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-2999:Notch1-2-WT 2

text: ArrayExpress

text: H-2 Db-NP366-374+ CD8+ T cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Notch1-2-WT 2


E-MTAB-2999:Notch1-2-WT 1

characteristic: ENA-FIRST-PUBLIC

text: Sanquin Blood Supply

text: public

text: E-MTAB-2999:Notch1-2-WT 1

text: ArrayExpress

text: H-2 Db-NP366-374+ CD8+ T cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Notch1-2-WT 1

characteristic: title


E-MTAB-2999:TEC 2

text: Sanquin Blood Supply

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-2999:TEC 2

text: ArrayExpress

text: KLRG1+ CD127- H-2 Db-NP366-374+ CD8+ T cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: TEC 2


E-MTAB-2999:Notch1-2-WT 3

text: Sanquin Blood Supply

text: public

characteristic: SRA accession

text: E-MTAB-2999:Notch1-2-WT 3

characteristic: Submitter Id

text: ArrayExpress

text: H-2 Db-NP366-374+ CD8+ T cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Notch1-2-WT 3


E-MTAB-2999:MPC 1

text: Sanquin Blood Supply

text: public

text: E-MTAB-2999:MPC 1

text: ArrayExpress

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: strain

text: MPC 1


E-MTAB-2999:Notch1-2-KO 1

characteristic: ENA-LAST-UPDATE

text: Sanquin Blood Supply

text: public

text: E-MTAB-2999:Notch1-2-KO 1

text: ArrayExpress

text: H-2 Db-NP366-374+ CD8+ T cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Notch1-2-KO 1


E-MTAB-2999:TEC 1

characteristic: External Id

text: Sanquin Blood Supply

text: public

text: E-MTAB-2999:TEC 1

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: TEC 1


E-MTAB-3007:A17 LCO WT003-

text: public

text: E-MTAB-3007:A17 LCO WT003-

tag: Namespace:Wageningen University, Laboratory of Molecular Biology

text: ArrayExpress

characteristic: broker name

text: barrel medic

text: Protocols: Growth conditions LCO application Illumina Truseq (Transcriptome)

text: wild type genotype

characteristic: genotype

text: Medicago truncatula

text: Medicago truncatula

text: Susceptible zone

characteristic: organism part

text: Medicago truncatula

text: Rhizobium LCOs

characteristic: stimulus

text: A17 LCO WT003-


E-MTAB-3007:Mtcre1 LCO WT003+

characteristic: ENA-CHECKLIST

text: Wageningen University, Laboratory of Molecular Biology

text: public

text: E-MTAB-3007:Mtcre1 LCO WT003+

text: ArrayExpress

text: barrel medic

characteristic: description

text: Mtcre1 mutant

text: Medicago truncatula

characteristic: organism

text: Medicago truncatula

text: Susceptible zone

text: Medicago truncatula

text: Rhizobium LCOs

text: Mtcre1 LCO WT003+


E-MTAB-3007:Mtcre1 noLCO WT001-

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-3007:Mtcre1 noLCO WT001-

text: ArrayExpress

text: barrel medic

text: Mtcre1 mutant

text: Medicago truncatula

text: Medicago truncatula

text: Susceptible zone

text: Medicago truncatula

text: Rhizobium LCOs (Control)

text: Mtcre1 noLCO WT001-


E-MTAB-3007:Mtcre1 noLCO WT002-

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3007:Mtcre1 noLCO WT002-

text: ArrayExpress

text: barrel medic

text: Mtcre1 mutant

text: Medicago truncatula

text: Medicago truncatula

text: Susceptible zone

text: Medicago truncatula

text: Rhizobium LCOs (Control)

text: Mtcre1 noLCO WT002-

characteristic: title


E-MTAB-3007:A17 LCO WT003+

text: public

characteristic: SRA accession

text: E-MTAB-3007:A17 LCO WT003+

characteristic: Submitter Id

text: ArrayExpress

text: barrel medic

characteristic: common name

text: wild type genotype

text: Medicago truncatula

text: Medicago truncatula

text: Susceptible zone

text: Medicago truncatula

text: Rhizobium LCOs

text: A17 LCO WT003+


E-MTAB-3007:Mtcre1 LCO WT001+

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-3007:Mtcre1 LCO WT001+

text: ArrayExpress

text: barrel medic

text: Mtcre1 mutant

text: Medicago truncatula

text: Medicago truncatula

text: Susceptible zone

text: Medicago truncatula

text: Rhizobium LCOs

text: Mtcre1 LCO WT001+


E-MTAB-3007:Mtcre1 LCO WT002-

text: public

text: E-MTAB-3007:Mtcre1 LCO WT002-

text: ArrayExpress

characteristic: broker name

text: barrel medic

text: Mtcre1 mutant

characteristic: genotype

text: Medicago truncatula

text: Medicago truncatula

text: Susceptible zone

text: Medicago truncatula

text: Rhizobium LCOs

text: Mtcre1 LCO WT002-


E-MTAB-3007:Mtcre1 noLCO WT003+

text: public

text: E-MTAB-3007:Mtcre1 noLCO WT003+

text: ArrayExpress

text: barrel medic

text: Mtcre1 mutant

text: Medicago truncatula

text: Medicago truncatula

text: Susceptible zone

characteristic: organism part

text: Medicago truncatula

text: Rhizobium LCOs (Control)

characteristic: stimulus

text: Mtcre1 noLCO WT003+


E-MTAB-3007:A17 noLCO WT002-

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-3007:A17 noLCO WT002-

text: ArrayExpress

text: barrel medic

characteristic: description

text: wild type genotype

text: Medicago truncatula

text: Medicago truncatula

text: Susceptible zone

text: Medicago truncatula

text: Rhizobium LCOs (Control)

text: A17 noLCO WT002-


E-MTAB-3007:A17 LCO WT001+

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-3007:A17 LCO WT001+

text: ArrayExpress

text: barrel medic

text: wild type genotype

text: Medicago truncatula

characteristic: organism

text: Medicago truncatula

text: Susceptible zone

text: Medicago truncatula

text: Rhizobium LCOs

text: A17 LCO WT001+


E-MTAB-3007:Mtcre1 noLCO WT002+

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-3007:Mtcre1 noLCO WT002+

text: ArrayExpress

text: barrel medic

text: Mtcre1 mutant

text: Medicago truncatula

text: Medicago truncatula

text: Susceptible zone

text: Medicago truncatula

text: Rhizobium LCOs (Control)

text: Mtcre1 noLCO WT002+


E-MTAB-3007:A17 noLCO WT001+

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3007:A17 noLCO WT001+

text: ArrayExpress

text: barrel medic

text: wild type genotype

text: Medicago truncatula

text: Medicago truncatula

text: Susceptible zone

text: Medicago truncatula

text: Rhizobium LCOs (Control)

text: A17 noLCO WT001+


E-MTAB-3007:Mtcre1 LCO WT001-

text: public

characteristic: SRA accession

text: E-MTAB-3007:Mtcre1 LCO WT001-

text: ArrayExpress

text: barrel medic

text: Mtcre1 mutant

text: Medicago truncatula

text: Medicago truncatula

text: Susceptible zone

text: Medicago truncatula

text: Rhizobium LCOs

text: Mtcre1 LCO WT001-

characteristic: title


E-MTAB-3007:Mtcre1 LCO WT002+

text: public

text: E-MTAB-3007:Mtcre1 LCO WT002+

characteristic: Submitter Id

text: ArrayExpress

text: barrel medic

characteristic: common name

text: Mtcre1 mutant

text: Medicago truncatula

text: Medicago truncatula

text: Susceptible zone

text: Medicago truncatula

text: Rhizobium LCOs

text: Mtcre1 LCO WT002+


E-MTAB-3007:Mtcre1 noLCO WT003-

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-3007:Mtcre1 noLCO WT003-

text: ArrayExpress

text: barrel medic

text: Mtcre1 mutant

text: Medicago truncatula

text: Medicago truncatula

text: Susceptible zone

text: Medicago truncatula

text: Rhizobium LCOs (Control)

text: Mtcre1 noLCO WT003-


E-MTAB-3007:A17 noLCO WT003+

text: public

text: E-MTAB-3007:A17 noLCO WT003+

text: ArrayExpress

characteristic: broker name

text: barrel medic

text: wild type genotype

characteristic: genotype

text: Medicago truncatula

text: Medicago truncatula

text: Susceptible zone

text: Medicago truncatula

text: Rhizobium LCOs (Control)

text: A17 noLCO WT003+


E-MTAB-3007:A17 noLCO WT001-

text: public

text: E-MTAB-3007:A17 noLCO WT001-

text: ArrayExpress

text: barrel medic

text: wild type genotype

text: Medicago truncatula

text: Medicago truncatula

text: Susceptible zone

characteristic: organism part

text: Medicago truncatula

text: Rhizobium LCOs (Control)

characteristic: stimulus

text: A17 noLCO WT001-


E-MTAB-3007:A17 LCO WT002+

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-3007:A17 LCO WT002+

text: ArrayExpress

text: barrel medic

characteristic: description

text: wild type genotype

text: Medicago truncatula

text: Medicago truncatula

text: Susceptible zone

text: Medicago truncatula

text: Rhizobium LCOs

text: A17 LCO WT002+


E-MTAB-3007:Mtcre1 LCO WT003-

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-3007:Mtcre1 LCO WT003-

text: ArrayExpress

text: barrel medic

text: Mtcre1 mutant

text: Medicago truncatula

characteristic: organism

text: Medicago truncatula

text: Susceptible zone

text: Medicago truncatula

text: Rhizobium LCOs

text: Mtcre1 LCO WT003-


E-MTAB-3007:A17 noLCO WT002+

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-3007:A17 noLCO WT002+

text: ArrayExpress

text: barrel medic

text: wild type genotype

text: Medicago truncatula

text: Medicago truncatula

text: Susceptible zone

text: Medicago truncatula

text: Rhizobium LCOs (Control)

text: A17 noLCO WT002+


E-MTAB-3007:Mtcre1 noLCO WT001+

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3007:Mtcre1 noLCO WT001+

text: ArrayExpress

text: barrel medic

text: Mtcre1 mutant

text: Medicago truncatula

text: Medicago truncatula

text: Susceptible zone

text: Medicago truncatula

text: Rhizobium LCOs (Control)

text: Mtcre1 noLCO WT001+


E-MTAB-3007:A17 LCO WT001-

text: public

characteristic: SRA accession

text: E-MTAB-3007:A17 LCO WT001-

text: ArrayExpress

text: barrel medic

text: wild type genotype

text: Medicago truncatula

text: Medicago truncatula

text: Susceptible zone

text: Medicago truncatula

text: Rhizobium LCOs

text: A17 LCO WT001-

characteristic: title


E-MTAB-3007:A17 LCO WT002-

text: public

text: E-MTAB-3007:A17 LCO WT002-

characteristic: Submitter Id

text: ArrayExpress

text: barrel medic

characteristic: common name

text: wild type genotype

text: Medicago truncatula

text: Medicago truncatula

text: Susceptible zone

text: Medicago truncatula

text: Rhizobium LCOs

text: A17 LCO WT002-


E-MTAB-3007:A17 noLCO WT003-

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-3007:A17 noLCO WT003-

text: ArrayExpress

text: barrel medic

text: wild type genotype

text: Medicago truncatula

text: Medicago truncatula

text: Susceptible zone

text: Medicago truncatula

text: Rhizobium LCOs (Control)

text: A17 noLCO WT003-


text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: house mouse

text: Mus musculus

text: ChiP DNA

characteristic: sample description

text: Mus musculus


text: male

characteristic: ArrayExpress-Sex

text: Homo sapiens

text: SC

text: public

text: pKLV2_U6gRNA5_PGKpuroBFP_Human_v1_library_replicate_1-sc-1927816

text: human

text: Homo sapiens

text: Pooled PCR products

text: Homo sapiens


text: male

text: Homo sapiens

characteristic: ENA-CHECKLIST

text: SC

text: public

text: pKLV2_U6gRNA5_PGKpuroBFP_Human_v1_library_replicate_2-sc-1927817

text: human

text: Homo sapiens

text: Pooled PCR products

text: Homo sapiens


text: male

text: Homo sapiens

text: SC

text: public

text: Colon_HT29_Cas9_library_1_day_6_post_infection_w_o_treatment-sc-2106110

text: human

text: Homo sapiens

text: Pooled PCR products

text: Homo sapiens


text: male

text: Homo sapiens

text: SC

text: public

text: Melanoma_M14_w_o_Cas9_for_library_representation-sc-2106108

text: human

text: Homo sapiens

text: Pooled PCR products

text: Homo sapiens


text: male

text: Homo sapiens

text: SC

text: public

text: Melanoma_M14w__Cas9_day_30_post_infection__w_o_treatment-sc-2106109

text: human

text: Homo sapiens

text: Pooled PCR products

text: Homo sapiens


text: male

text: Homo sapiens

text: SC

text: public

text: Colon_HT29_Cas9_library_2_day_6_post_infection_w_o_treatment-sc-2106111

text: human

text: Homo sapiens

text: Pooled PCR products

text: Homo sapiens


text: male

text: Homo sapiens

text: SC

text: public

text: Colon_HT29_Cas9_library_3_day_6_post_infection_w_o_treatment-sc-2106112

text: human

text: Homo sapiens

text: Pooled PCR products

text: Homo sapiens


text: male

text: Homo sapiens

text: SC

text: public

text: Colon_HT29_Cas9_library_4_day_6_post_infection_w_o_treatment-sc-2106113

text: human

text: Homo sapiens

text: Pooled PCR products

text: Homo sapiens


text: male

text: Homo sapiens

text: SC

text: public

text: Colon_HT29_Cas9_library_1_day_16_post_infection_w_o_treatment-sc-2106114

text: human

text: Homo sapiens

text: Pooled PCR products

text: Homo sapiens


text: male

text: Homo sapiens

text: SC

text: public

text: Colon_HT29_Cas9_library_2_day_16_post_infection_w_o_treatment-sc-2106115

text: human

text: Homo sapiens

text: Pooled PCR products

text: Homo sapiens


text: male

text: Homo sapiens

text: SC

text: public

text: Colon_HT29_Cas9_library_3_day_16_post_infection_w_o_treatment-sc-2106116

text: human

text: Homo sapiens

text: Pooled PCR products

text: Homo sapiens


text: male

text: Homo sapiens

text: SC

text: public

text: Colon_HT29_Cas9_library_4_day_16_post_infection_w_o_treatment-sc-2106117

text: human

text: Homo sapiens

text: Pooled PCR products

text: Homo sapiens


text: male

text: Homo sapiens

text: SC

text: public

text: Melanoma_M14___alpha_toxin_resistant-sc-2106214

text: human

text: Homo sapiens

text: Pooled PCR products

text: Homo sapiens


text: male

text: Homo sapiens

text: SC

text: public

text: Colon_HT29_Cas9_library_1___alpha_toxin_resistant-sc-2106215

text: human

text: Homo sapiens

text: Pooled PCR products

text: Homo sapiens


text: male

text: Homo sapiens

text: SC

text: public

text: Colon_HT29_Cas9_library_2___alpha_toxin_resistant-sc-2106216

text: human

text: Homo sapiens

text: Pooled PCR products

text: Homo sapiens


text: male

text: Homo sapiens

text: SC

text: public

text: Colon_HT29_Cas9_library_3___alpha_toxin_resistant-sc-2106217

text: human

text: Homo sapiens

text: Pooled PCR products

text: Homo sapiens


text: male

text: Homo sapiens

text: SC

text: public

text: Colon_HT29_Cas9_library_4___alpha_toxin_resistant-sc-2106218

text: human

text: Homo sapiens

text: Pooled PCR products

text: Homo sapiens


E-MTAB-3009:wild type #3

text: public

text: E-MTAB-3009:wild type #3

tag: Namespace:Department of Plant Sciences, University of Cambridge

text: 5 weeks post germination; 2 weeks post infection

characteristic: age

text: ArrayExpress

characteristic: broker name

text: thale cress

text: fwa-d epimutant Protocols: Arabidopsis growth Virus infection Trizol Illumina TruSeq Small RNA cloning kit

characteristic: description

text: Rosette leaf

characteristic: developmental stage

characteristic: ecotype

text: Long days (16h:8h); 21 deg; infected at 3 weeks of age

characteristic: environmental history

text: wild type genotype

characteristic: genotype

text: RNA PCR Primer, Index 14

characteristic: index primer used for pcr

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: wild type #3


E-MTAB-3009:dcl2/4 #3

characteristic: ENA-FIRST-PUBLIC

text: Department of Plant Sciences, University of Cambridge

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-3009:dcl2/4 #3

text: ArrayExpress

text: thale cress

text: fwa-d epimutant introgressed Protocols: Arabidopsis growth Virus infection Trizol Illumina TruSeq Small RNA cloning kit

text: Rosette leaf

text: RNA PCR Primer, Index 23

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: dcl2/4 #3

characteristic: title


E-MTAB-3009:dcl2/4 #1

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-3009:dcl2/4 #1

characteristic: Submitter Id

text: ArrayExpress

text: thale cress

characteristic: common name

text: Rosette leaf

text: RNA PCR Primer, Index 4

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: dcl2/4 #1


E-MTAB-3009:dcl2/4 #2

text: public

text: E-MTAB-3009:dcl2/4 #2

characteristic: age

text: ArrayExpress

characteristic: broker name

text: thale cress

characteristic: description

text: Rosette leaf

characteristic: developmental stage

characteristic: ecotype

text: RNA PCR Primer, Index 21

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: dcl2/4 #2


E-MTAB-3009:wild type #2

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

text: public

text: E-MTAB-3009:wild type #2

text: ArrayExpress

text: thale cress

text: Rosette leaf

characteristic: environmental history

text: wild type genotype

characteristic: genotype

text: RNA PCR Primer, Index 13

characteristic: index primer used for pcr

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: wild type #2


E-MTAB-3009:wild type #1

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-3009:wild type #1

text: ArrayExpress

text: thale cress

text: Rosette leaf

text: wild type genotype

text: RNA PCR Primer, Index 2

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: wild type #1


E-MTAB-3009:wild type #4

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-3009:wild type #4

characteristic: Submitter Id

text: ArrayExpress

text: thale cress

text: Rosette leaf

text: wild type genotype

text: RNA PCR Primer, Index 15

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: wild type #4

characteristic: title


E-MTAB-3009:dcl2/4 #4

text: public

text: E-MTAB-3009:dcl2/4 #4

characteristic: age

text: ArrayExpress

characteristic: broker name

text: thale cress

characteristic: common name

characteristic: description

text: Rosette leaf

characteristic: developmental stage

text: RNA PCR Primer, Index 24

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: dcl2/4 #4


text: Normal

characteristic: ArrayExpress-Phenotype

text: Mouse

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: male

characteristic: ArrayExpress-Sex

text: Homo sapiens

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 293_transduced_with_Mouse_V1_lentiviral_gRNA_library-sc-1997921

text: human

text: Homo sapiens

text: Pooled PCR products

characteristic: sample description

text: Homo sapiens


text: male

text: Homo sapiens

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: SRA accession

text: 293_transduced_with_Human_V1_lentiviral_gRNA_library-sc-1997922

text: human

text: Homo sapiens

characteristic: organism

text: Pooled PCR products

text: Homo sapiens


text: male

text: Homo sapiens

text: SC

text: public

text: 293_transduced_with_Human_V1_lentiviral_gRNA_library_replicate-sc-1997923

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

text: Pooled PCR products

text: Homo sapiens


text: male

text: Homo sapiens

text: SC

text: public

text: HeLa_transduced_with_Mouse_V1_lentiviral_gRNA_library-sc-1997924

text: human

text: Homo sapiens

text: Pooled PCR products

text: Homo sapiens


text: male

text: Homo sapiens

text: SC

text: public

text: HeLa_transduced_with_Human_V1_lentiviral_gRNA_library-sc-1997925

text: human

text: Homo sapiens

text: Pooled PCR products

text: Homo sapiens


text: Danio rerio

text: SC

text: public

text: zebrafish

text: Danio rerio

text: Danio rerio


E-MTAB-3020:Total RNA 2 - 0 min

text: public

text: E-MTAB-3020:Total RNA 2 - 0 min

tag: Namespace:Genome organization and Function German Cancer Research Center (DKFZ)

text: ArrayExpress

characteristic: broker name

text: HUVEC cell line

characteristic: cell line

text: human

text: Protocols: Cell were treated with the pro-inflammatory cytokine TNFa for 0 or 30 min. Short and long RNA fractions were separated and DNase-treated after cell fractionation starting with about 1.5x10e7 cells using the miRNeasy mini kit (qiagen). RNA fraction were transformed into cDNA library with solexa adaptors using the standard Illumina protocol. Libraries were prepared using the NEB library prep kit for long RNAs.

characteristic: description

text: Total RNA 2 - 0 min

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Total RNA 2 - 0 min

characteristic: title


E-MTAB-3020:Poly(A)+ RNA 1 -  30 min

characteristic: ENA-FIRST-PUBLIC

text: Genome organization and Function German Cancer Research Center (DKFZ)

characteristic: INSDC center name

text: public

text: E-MTAB-3020:Poly(A)+ RNA 1 - 30 min

text: ArrayExpress

text: HUVEC cell line

text: human

text: Protocols: Cell were treated with the pro-inflammatory cytokine TNFa for 0 or 30 min. Short and long RNA fractions were separated and DNase-treated after cell fractionation starting with about 1.5x10e7 cells using the miRNeasy mini kit (qiagen). RNA fraction were transformed into cDNA library with solexa adaptors using the standard Illumina protocol. Libraries were prepared using the Nugen multiplex library prep kit.

text: Poly(A)+ RNA 1 - 30 min

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Poly(A)+ RNA 1 - 30 min


E-MTAB-3020:Factory RNA 3 -  0 min

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-3020:Factory RNA 3 - 0 min

text: ArrayExpress

text: HUVEC cell line

text: human

text: Protocols: Cell were treated with the pro-inflammatory cytokine TNFa for 0 or 30 min. Short and long RNA fractions were separated and DNase-treated after cell fractionation starting with about 1.5x10e7 cells using the miRNeasy mini kit (qiagen). RNA fraction were transformed into cDNA library with solexa adaptors using the standard Illumina protocol. Libraries were prepared using the NEB library prep kit for short RNAs.

text: Factory RNA 3 - 0 min

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Factory RNA 3 - 0 min


E-MTAB-3020:Poly(A)+ RNA 1 -  0 min

text: public

characteristic: INSDC status

text: E-MTAB-3020:Poly(A)+ RNA 1 - 0 min

text: ArrayExpress

text: HUVEC cell line

text: human

text: Poly(A)+ RNA 1 - 0 min

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Poly(A)+ RNA 1 - 0 min


E-MTAB-3020:Total RNA 1 - 30 min

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-3020:Total RNA 1 - 30 min

text: ArrayExpress

text: HUVEC cell line

text: human

text: Total RNA 1 - 30 min

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Total RNA 1 - 30 min


E-MTAB-3020:Factory RNA 2 - 0 min

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-3020:Factory RNA 2 - 0 min

text: ArrayExpress

text: HUVEC cell line

text: human

text: Factory RNA 2 - 0 min

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Factory RNA 2 - 0 min


E-MTAB-3020:Factory RNA 2 - 30 min

characteristic: External Id

text: public

text: E-MTAB-3020:Factory RNA 2 - 30 min

text: ArrayExpress

text: HUVEC cell line

text: human

text: Factory RNA 2 - 30 min

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Factory RNA 2 - 30 min


E-MTAB-3020:Total RNA 2 - 30 min

text: public

characteristic: SRA accession

text: E-MTAB-3020:Total RNA 2 - 30 min

text: ArrayExpress

text: HUVEC cell line

text: human

text: Total RNA 2 - 30 min

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Total RNA 2 - 30 min


E-MTAB-3020:Chromatin RNA - 30 min

text: public

text: E-MTAB-3020:Chromatin RNA - 30 min

text: ArrayExpress

text: HUVEC cell line

text: human

text: Chromatin RNA - 30 min

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: Chromatin RNA - 30 min


E-MTAB-3020:Factory RNA 1 - 30 min

text: public

text: E-MTAB-3020:Factory RNA 1 - 30 min

characteristic: Submitter Id

text: ArrayExpress

text: HUVEC cell line

text: human

text: Factory RNA 1 - 30 min

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Factory RNA 1 - 30 min


E-MTAB-3020:Factory RNA 3 -  30 min

text: public

text: E-MTAB-3020:Factory RNA 3 - 30 min

text: ArrayExpress

text: HUVEC cell line

text: human

characteristic: common name

text: Factory RNA 3 - 30 min

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Factory RNA 3 - 30 min


E-MTAB-3020:Total RNA 1 -  0 min

text: public

text: E-MTAB-3020:Total RNA 1 - 0 min

text: ArrayExpress

characteristic: broker name

text: HUVEC cell line

text: human

text: Total RNA 1 - 0 min

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Total RNA 1 - 0 min


E-MTAB-3020:Poly(A)+ RNA 2 -  30 min

text: public

text: E-MTAB-3020:Poly(A)+ RNA 2 - 30 min

text: ArrayExpress

text: HUVEC cell line

characteristic: cell line

text: human

text: Poly(A)+ RNA 2 - 30 min

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Poly(A)+ RNA 2 - 30 min


E-MTAB-3020:Chromatin RNA - 0 min

text: public

text: E-MTAB-3020:Chromatin RNA - 0 min

text: ArrayExpress

text: HUVEC cell line

text: human

characteristic: description

text: Chromatin RNA - 0 min

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Chromatin RNA - 0 min


E-MTAB-3020:Poly(A)+ RNA 2 -  0 min

text: public

text: E-MTAB-3020:Poly(A)+ RNA 2 - 0 min

text: ArrayExpress

text: HUVEC cell line

text: human

text: Poly(A)+ RNA 2 - 0 min

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Poly(A)+ RNA 2 - 0 min


E-MTAB-3020:Total RNA 3 -  30 min

text: public

text: E-MTAB-3020:Total RNA 3 - 30 min

text: ArrayExpress

text: HUVEC cell line

text: human

text: Total RNA 3 - 30 min

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Total RNA 3 - 30 min

characteristic: title


E-MTAB-3020:Total RNA 3 -  0 min

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-3020:Total RNA 3 - 0 min

text: ArrayExpress

text: HUVEC cell line

text: human

text: Total RNA 3 - 0 min

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Total RNA 3 - 0 min


E-MTAB-3020:Factory RNA 1 - 0 min

characteristic: INSDC center name

text: public

text: E-MTAB-3020:Factory RNA 1 - 0 min

text: ArrayExpress

text: HUVEC cell line

text: human

text: Factory RNA 1 - 0 min

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Factory RNA 1 - 0 min


characteristic: INSDC first public

text: public

tag: Namespace:Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium Department of Plant Systems Biology,VIB, Gent, Belgium

text: ArrayExpress

text: thale cress

text: Protocols: Adapter ligation; Gel fractionating

characteristic: genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium Department of Plant Systems Biology,VIB, Gent, Belgium

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: Hatching:Long pec - ZFS:0000033

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at hatching - long pec stage (48 hpf) plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGTCTATC) is bases 13 to 20 of read 1 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain