text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:49Z-1607047

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


status: PUBLIC

text: Human

tag: attribute

characteristic: ArrayExpress-Species

text: Promega

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

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

characteristic: SRA accession

text: Homo_sapiens-sc-2013-04-03T15:18:52Z-1607050

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: genomic DNA

characteristic: sample description

text: Homo sapiens

text: Promega

characteristic: strain


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:55Z-1607053

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:58Z-1607056

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:01Z-1607059

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:04Z-1607062

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:07Z-1607065

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:13Z-1607071

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:16Z-1607074

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:19Z-1607077

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:22Z-1607080

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:25Z-1607083

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:28Z-1607086

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:31Z-1607089

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:34Z-1607092

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:37Z-1607095

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:40Z-1607098

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:43Z-1607101

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:47Z-1607104

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:50Z-1607107

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:54Z-1607110

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Larval: protruding mouth: ZFS:0000035 - Larval: Day 4:ZFS:0000036

characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_14_1_sibling-sc-2013-04-02T11:26:11Z-1605408

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal embryos from ZMP phenotype 14 clutch 1. A 5 base indexing sequence (AGAAG) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph14

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

text: SC

text: public

text: ZMP_phenotype_14_5_mutant-sc-2013-04-02T11:26:15Z-1605411

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 14 clutch 5. A 5 base indexing sequence (AACCG) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph14

text: Danio rerio

text: mixed


text: CEA

text: public

text: ArrayExpress

characteristic: broker name

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 except for Rad2-HA strain. 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: MATa ura3-52 his3-D200 ade2-101uaa trp1-D63 lys2-801uag leu2-D1 med17::KanMX6 // MED17 CEN TRP1

characteristic: genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a

characteristic: sex

characteristic: title

type: has member


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CEA

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

characteristic: genetic modification

text: MATa ura3-52 his3-D200 ade2-101uaa trp1-D63 lys2-801uag leu2-D1 RAD3::3HA::HIS3 med17::KanMX6 // MED17 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


text: CEA

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: baker's yeast

characteristic: common name

text: tagging

text: MATa ura3-52 his3-D200 ade2-101uaa trp1-D63 lys2-801uag leu2-D1 MED15::3HA::HIS3 med17::KanMX6 // MED17 CEN TRP1

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


text: CEA

text: public

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-D200 ade2-101uaa trp1-D63 lys2-801uag leu2-D1 MED5::3HA::HIS3

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a

characteristic: strain

text: INPUT-WT


text: CEA

text: public

text: ArrayExpress

text: baker's yeast

characteristic: description

text: tagging

text: MATa ura3-52 his3-D200 ade2-101uaa trp1-D63 lys2-801uag leu2-D1 KIN28::3HA::HIS3 med17::KanMX6 // MED17 CEN TRP1

characteristic: genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


text: CEA

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-D200 ade2-101uaa trp1-D63 lys2-801uag leu2-D1 MED5::3HA::HIS med17::KanMX6 // MED17 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a

characteristic: sex

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: CEA

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-D200 ade2-101uaa trp1-D63 lys2-801uag leu2-D1 HIS3::3HA::RAD2

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a


characteristic: External Id

text: CEA

characteristic: INSDC center name

text: public

text: ArrayExpress

text: baker's yeast

text: tagging

text: MATa ura3-52 his3-D200 ade2-101uaa trp1-D63 lys2-801uag leu2-D1 LEU2::3HA::SPT15 med17::KanMX6 // MED17 CEN TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: mating type a

text: TBP-WT-IP


text: Human

characteristic: ArrayExpress-Species

text: Promega

characteristic: ArrayExpress-StrainOrLine

text: SC

characteristic: INSDC first public

text: public

text: Homo_sapiens-sc-2013-04-03T15:14:58Z-1606920

text: human

text: Homo sapiens

text: genomic DNA

characteristic: sample description

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Homo_sapiens-sc-2013-04-03T15:15:39Z-1606922

characteristic: Submitter Id

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:13Z-1606927

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: genomic DNA

text: Homo sapiens

text: Promega

characteristic: strain


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:15Z-1606928

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:18Z-1606931

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:22Z-1606934

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:25Z-1606937

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:29Z-1606940

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:33Z-1606943

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:36Z-1606946

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:39Z-1606949

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:43Z-1606952

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:47Z-1606955

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:50Z-1606958

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:53Z-1606961

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:56Z-1606964

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:59Z-1606967

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:02Z-1606970

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:05Z-1606973

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:10Z-1606976

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:15Z-1606979

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:19Z-1606982

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:25Z-1606985

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:29Z-1606988

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:34Z-1606991

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:38Z-1606994

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:45Z-1606997

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:49Z-1607000

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:52Z-1607003

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:59Z-1607009

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:03Z-1607012

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:08Z-1607015

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:13Z-1607018

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:17Z-1607021

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:22Z-1607024

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:28Z-1607027

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:32Z-1607030

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:35Z-1607033

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:41Z-1607039

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

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text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:09Z-1606925

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:16Z-1606929

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:20Z-1606932

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:23Z-1606935

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:27Z-1606938

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:30Z-1606941

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:34Z-1606944

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:37Z-1606947

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:41Z-1606950

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:45Z-1606953

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:48Z-1606956

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:51Z-1606959

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:54Z-1606962

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:16:57Z-1606965

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:00Z-1606968

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:03Z-1606971

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:07Z-1606974

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:12Z-1606977

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:16Z-1606980

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:21Z-1606983

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:26Z-1606986

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Institut de la Recherche Agronomique

text: public

tag: Namespace:Institut de la Recherche Agronomique

characteristic: biological replicate

text: ArrayExpress

characteristic: broker name

text: oocyte

characteristic: cell type

text: sheep

text: Protocols: Laser Capture Microdissection from Transcriptome profiling of sheep granulosa cells and oocytes during early follicular development obtained by Laser Capture Microdissection Bonnet et al 2010 (doi: 10.1186/1471-2164-12-417) RNA extraction from Transcriptome profiling of sheep granulosa cells and oocytes during early follicular development obtained by Laser Capture Microdissection Bonnet et al 2010 (doi: 10.1186/1471-2164-12-417) T7 linear amplification from Transcriptome profiling of sheep granulosa cells and oocytes during early follicular development obtained by Laser Capture Microdissection Bonnet et al 2010 (doi: 10.1186/1471-2164-12-417) All RNAseq libraries were constructed from 200 ng of aRNA using Illumina TruSeq RNA Sample Prep (Illumina, San Diego, CA USA) following manufacturers instruction. Each biological replicate was identified by a different index. Libraries were quantified using QPCR NGS Library Quant Kit (Agilent). Three libraries were pooled and loaded randomly per lane at 8 pM concentration.

characteristic: description

text: primordial follicle

characteristic: developmental stage

text: Ovis aries

text: Ovis aries

text: ovary

characteristic: organism part

text: Ovis aries

text: female

characteristic: sex

text: frozen specimen

characteristic: specimen with known storage state


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institut de la Recherche Agronomique

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: oocyte

text: sheep

text: secondary follicle

text: Ovis aries

text: Ovis aries

text: ovary

text: Ovis aries

text: female

text: frozen specimen

characteristic: title


text: Institut de la Recherche Agronomique

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: granulosa cell

text: sheep

characteristic: common name

text: secondary follicle

text: Ovis aries

text: Ovis aries

text: ovary

text: Ovis aries

text: female

text: frozen specimen


text: Institut de la Recherche Agronomique

text: public

characteristic: biological replicate

text: ArrayExpress

characteristic: broker name

text: sheep

text: Protocols: The thirteen tissue samples (foetal ovary, pituitary gland, hypothalamus, muscle, skin, heart, lung, intestine, stomach, kidney, spleen, liver and theca) were sampled at the local slaughterhouse from 3 individual animals, frozen in liquid nitrogen and stored at -80C until RNA extraction. Total RNA was isolated using the Nucleospin RNA II kit (Macherey-Nagel GmbH & Co, ref 740 955 50, HOERDT, France). The 12 total RNA tissue samples (except foetal ovary) were pooled into 3 independent groups. T7 linear amplification from Transcriptome profiling of sheep granulosa cells and oocytes during early follicular development obtained by Laser Capture Microdissection Bonnet et al 2010 (doi: 10.1186/1471-2164-12-417) All RNAseq libraries were constructed from 200 ng of aRNA using Illumina TruSeq RNA Sample Prep (Illumina, San Diego, CA USA) following manufacturers instruction. Each biological replicate was identified by a different index. Libraries were quantified using QPCR NGS Library Quant Kit (Agilent). Three libraries were pooled and loaded randomly per lane at 8 pM concentration.

text: Ovis aries

characteristic: organism

text: Ovis aries

text: Ovis aries

text: female

text: frozen specimen


text: Institut de la Recherche Agronomique

text: public

text: ArrayExpress

text: granulosa cell

characteristic: cell type

text: sheep

characteristic: description

text: primordial follicle

characteristic: developmental stage

text: Ovis aries

text: Ovis aries

text: ovary

characteristic: organism part

text: Ovis aries

text: female

text: frozen specimen


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Institut de la Recherche Agronomique

text: public

text: ArrayExpress

text: granulosa cell

text: sheep

text: primary follicle

text: Ovis aries

text: Ovis aries

text: ovary

text: Ovis aries

text: female

characteristic: sex

text: frozen specimen

characteristic: specimen with known storage state


characteristic: External Id

text: Institut de la Recherche Agronomique

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: oocyte

text: sheep

text: primary follicle

text: Ovis aries

text: Ovis aries

text: ovary

text: Ovis aries

text: female

text: frozen specimen

characteristic: title


text: Institut de la Recherche Agronomique

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: granulosa cell

text: sheep

text: small antrum follicle

text: Ovis aries

text: Ovis aries

text: ovary

text: Ovis aries

text: female

text: frozen specimen


text: Institut de la Recherche Agronomique

text: public

characteristic: biological replicate

text: ArrayExpress

characteristic: broker name

text: oocyte

text: sheep

characteristic: common name

text: small antrum follicle

text: Ovis aries

characteristic: organism

text: Ovis aries

text: ovary

text: Ovis aries

text: female

text: frozen specimen


text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: DBA_2J_DT2N1-sc-2013-04-10T14:56:14Z-1610226

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mus musculus

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: DBA_2J_DT2N2-sc-2013-04-10T14:56:15Z-1610227

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mus musculus

text: SC

text: public

text: LP_J_DT1N1-sc-2013-04-10T14:56:16Z-1610228

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mus musculus

text: SC

text: public

text: LP_J_DT1N2-sc-2013-04-10T14:56:17Z-1610229

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

tag: Namespace:Biomedical Center, University of Iceland

text: ArrayExpress

characteristic: cell line

text: house mouse

text: Protocols: P19 embryonal carcinoma cells were cultured in DMEM with 10% fetal calf serum, The mouse P19ECs were obtained from ATCC and were cultured in DMEM, 10% fetal 655 calf serum, 2mM L-glutamine (Gibco) and 50 ug/ml penicillin/streptomycin (Gibco) P19ECs were co-transfected with TRE-Tight BLIMP1-EGFP, and and pCAG-tTA-IP using Lipofectamine 2000 (Invitrogen) according to the manufacturer's instructions. The cells were harvested and crosslinked with 1% formaldehyde 24 hours after transfection. Phenol Chloroform extraction Performed ChIP according to: Magnusdottir, E. et al. Epidermal terminal differentiation depends on B lymphocyte912 induced maturation protein-1. Proceedings of the National Academy of Sciences of the United States of America 104, 14988-93 (2007). Libraries were generated using Illumina ChIPseq DNA Sample 665 Preparation Kit, (cat. No 1003473)

characteristic: description

text: epiblast

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: wild type

characteristic: phenotype

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state


characteristic: External Id

text: Biomedical Center, University of Iceland

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: house mouse

text: epiblast

text: Mus musculus

text: Mus musculus

text: wild type

text: Mus musculus

text: fresh specimen

characteristic: title


E-MTAB-1600:Culture 1

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-1600:Culture 1

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: epiblast

characteristic: cell type

text: house mouse

text: Protocols: P19 embryonal carcinoma cells were cultured in DMEM with 10% fetal calf serum. The mouse P19ECs were obtained from ATCC and were cultured in DMEM, 10% fetal 655 calf serum, 2mM L-glutamine (Gibco) and 50 ug/ml penicillin/streptomycin (Gibco) P19ECs were stably transfected with AP2gamma. Cells were harvested and crosslinked with 1% formaldehyde. Phenol Chloroform extraction Performed ChIP according to: Magnusdottir, E. et al. Epidermal terminal differentiation depends on B lymphocyte912 induced maturation protein-1. Proceedings of the National Academy of Sciences of the United States of America 104, 14988-93 (2007). Libraries were generated using Nugene Ovation Ultralow Library Kit.

text: Mus musculus

text: Mus musculus

text: wild type

text: Mus musculus

text: fresh specimen

text: Culture 1


text: male

characteristic: ArrayExpress-Sex

text: Homo Sapien

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: SC_KALASH5512018-sc-2013-04-09T13:16:00Z-1606422

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

text: Institut de la Recherche Agronomique

text: public

characteristic: biological replicate

text: ArrayExpress

text: oocyte

text: sheep

characteristic: description

text: primordial follicle

characteristic: developmental stage

text: Ovis aries

text: Ovis aries

text: ovary

characteristic: organism part

text: Ovis aries

text: female

characteristic: sex

text: frozen specimen


characteristic: External Id

text: Institut de la Recherche Agronomique

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: oocyte

text: sheep

text: secondary follicle

text: Ovis aries

text: Ovis aries

text: ovary

text: Ovis aries

text: female

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


text: Institut de la Recherche Agronomique

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: sheep

text: Ovis aries

text: Ovis aries

text: pituitary gland, hypothalamus, muscle, skin, heart, lung, intestine, stomach, kidney, spleen, liver and theca

text: Ovis aries

text: female

text: frozen specimen


characteristic: ENA-FIRST-PUBLIC

text: Institut de la Recherche Agronomique

text: public

text: ArrayExpress

text: granulosa cell

characteristic: cell type

text: sheep

characteristic: common name

text: secondary follicle

text: Ovis aries

characteristic: organism

text: Ovis aries

text: ovary

text: Ovis aries

text: female

text: frozen specimen


text: Larval: protruding mouth ZFS:0000035

characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: ZMP_phenotype_18_1_mutant-sc-2013-04-11T15:10:57Z-1610759

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 18 clutch 1. A 5 base indexing sequence (GAGGC) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph18

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Larval: protruding mouth ZFS:0000035

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ZMP_phenotype_18_1_sibling-sc-2013-04-11T15:11:01Z-1610760

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal embryos from ZMP phenotype 18 clutch 1. A 5 base indexing sequence (AGAAG) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph18

text: Danio rerio

text: mixed


text: Larval: protruding mouth ZFS:0000035

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ZMP_phenotype_18_2_mutant-sc-2013-04-11T15:11:03Z-1610761

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 18 clutch 2. A 5 base indexing sequence (CAGAG) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph18

text: Danio rerio

text: mixed


text: Larval: protruding mouth ZFS:0000035

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: ZMP_phenotype_18_2_sibling-sc-2013-04-11T15:11:05Z-1610762

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal embryos from ZMP phenotype 18 clutch 2. A 5 base indexing sequence (GCACG) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph18

text: Danio rerio

text: mixed


text: Larval: protruding mouth ZFS:0000035

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_18_3_mutant-sc-2013-04-11T15:11:07Z-1610763

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 18 clutch 3. A 5 base indexing sequence (CGCAA) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph18

text: Danio rerio

text: mixed


text: Larval: protruding mouth ZFS:0000035

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_18_3_sibling-sc-2013-04-11T15:11:09Z-1610764

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from morphologically normal embryos from ZMP phenotype 18 clutch 3. A 5 base indexing sequence (CAAGA) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph18

text: Danio rerio

text: mixed


text: Larval: protruding mouth ZFS:0000035

characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_19_1_mutant-sc-2013-04-11T15:11:10Z-1610765

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 19 clutch 1. A 5 base indexing sequence (GAGGC) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph19

text: Danio rerio

text: mixed


text: Larval: protruding mouth ZFS:0000035

text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_19_1_sibling-sc-2013-04-11T15:11:12Z-1610766

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal embryos from ZMP phenotype 19 clutch 1. A 5 base indexing sequence (AGAAG) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph19

text: Danio rerio

text: mixed


text: Larval: protruding mouth ZFS:0000035

text: Whole Embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

text: SC

text: public

text: ZMP_phenotype_19_2_mutant-sc-2013-04-11T15:11:14Z-1610767

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 19 clutch 2. A 5 base indexing sequence (CAGAG) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph19

text: Danio rerio

text: mixed


text: Larval: protruding mouth ZFS:0000035

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: ZMP_phenotype_19_2_sibling-sc-2013-04-11T15:11:16Z-1610768

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal embryos from ZMP phenotype 19 clutch 2. A 5 base indexing sequence (GCACG) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph19

text: Danio rerio

text: mixed


text: Larval: protruding mouth ZFS:0000035

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: ZMP_phenotype_19_3_mutant-sc-2013-04-11T15:11:18Z-1610769

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 19 clutch 3. A 5 base indexing sequence (CGCAA) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph19

text: Danio rerio

text: mixed


text: Larval: protruding mouth ZFS:0000035

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_19_3_sibling-sc-2013-04-11T15:11:20Z-1610770

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal embryos from ZMP phenotype 19 clutch 3. A 5 base indexing sequence (CAAGA) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph19

characteristic: sample description

text: Danio rerio

text: mixed


text: Larval: protruding mouth ZFS:0000035

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_19_4_mutant-sc-2013-04-11T15:11:22Z-1610771

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 19 clutch 4. A 5 base indexing sequence (GCCGA) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph19

text: Danio rerio

text: mixed

characteristic: strain


text: Larval: protruding mouth ZFS:0000035

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

text: public

text: ZMP_phenotype_19_4_sibling-sc-2013-04-11T15:11:23Z-1610772

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal embryos from ZMP phenotype 19 clutch 4. A 5 base indexing sequence (CGGCC) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph19

text: Danio rerio

text: mixed


text: Larval - day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

text: public

text: ZMP_phenotype_20_1_mutant-sc-2013-04-11T15:20:57Z-1610773

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 20 clutch 1. A 5 base indexing sequence (GAGGC) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph20

text: Danio rerio

text: mixed


text: Larval - day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC first public

text: public

text: ZMP_phenotype_20_1_sibling-sc-2013-04-11T15:21:01Z-1610774

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal sibling embryos from ZMP phenotype 20 clutch 1. A 5 base indexing sequence (AGAAG) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph20

text: Danio rerio

text: mixed


text: Larval - day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

text: ZMP_phenotype_20_2_mutant-sc-2013-04-11T15:21:03Z-1610775

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 20 clutch 2. A 5 base indexing sequence (CAGAG) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph20

text: Danio rerio

text: mixed


text: Larval - day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: INSDC status

text: ZMP_phenotype_20_2_sibling-sc-2013-04-11T15:21:05Z-1610776

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal sibling embryos from ZMP phenotype 20 clutch 2. A 5 base indexing sequence (GCACG) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph20

text: Danio rerio

text: mixed


text: Larval - day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

text: ZMP_phenotype_20_3_mutant-sc-2013-04-11T15:21:07Z-1610777

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 20 clutch 3. A 5 base indexing sequence (GCCGA) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph20

text: Danio rerio

text: mixed


text: Larval - day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_20_3_sibling-sc-2013-04-11T15:21:09Z-1610778

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal sibling embryos from ZMP phenotype 20 clutch 3. A 5 base indexing sequence (CGGCC) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph20

text: Danio rerio

text: mixed


text: Human

text: Promega

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:31Z-1606989

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:35Z-1606992

text: human

characteristic: common name

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:40Z-1606995

text: human

text: Homo sapiens

characteristic: organism

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:46Z-1606998

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:50Z-1607001

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:53Z-1607004

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:17:57Z-1607007

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:00Z-1607010

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:05Z-1607013

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:10Z-1607016

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:15Z-1607019

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:19Z-1607022

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:24Z-1607025

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:30Z-1607028

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:33Z-1607031

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:36Z-1607034

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:39Z-1607037

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:42Z-1607040

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:45Z-1607043

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:51Z-1607049

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:54Z-1607052

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Institut de la Recherche Agronomique

text: public

characteristic: biological replicate

text: ArrayExpress

characteristic: broker name

text: granulosa cell

characteristic: cell type

text: sheep

text: Protocols: Laser Capture Microdissection from Transcriptome profiling of sheep granulosa cells and oocytes during early follicular development obtained by Laser Capture Microdissection Bonnet et al 2010 (doi: 10.1186/1471-2164-12-417) RNA extraction from Transcriptome profiling of sheep granulosa cells and oocytes during early follicular development obtained by Laser Capture Microdissection Bonnet et al 2010 (doi: 10.1186/1471-2164-12-417) T7 linear amplification from Transcriptome profiling of sheep granulosa cells and oocytes during early follicular development obtained by Laser Capture Microdissection Bonnet et al 2010 (doi: 10.1186/1471-2164-12-417) All RNAseq libraries were constructed from 200 ng of aRNA using Illumina TruSeq RNA Sample Prep (Illumina, San Diego, CA USA) following manufacturers instruction. Each biological replicate was identified by a different index. Libraries were quantified using QPCR NGS Library Quant Kit (Agilent). Three libraries were pooled and loaded randomly per lane at 8 pM concentration.

characteristic: description

text: primordial follicle

characteristic: developmental stage

text: Ovis aries

text: Ovis aries

text: ovary

characteristic: organism part

text: Ovis aries

text: female

characteristic: sex

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institut de la Recherche Agronomique

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: oocyte

text: sheep

text: small antrum follicle

text: Ovis aries

text: Ovis aries

text: ovary

text: Ovis aries

text: female

text: frozen specimen


text: Larval - day 5 ZFS:0000037

characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ZMP_phenotype_20_4_sibling-sc-2013-04-11T15:21:13Z-1610780

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal sibling embryos from ZMP phenotype 20 clutch 4. A 5 base indexing sequence (ACGGG) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph20

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Larval - day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: ZMP_phenotype_20_5_mutant-sc-2013-04-11T15:21:15Z-1610781

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 20 clutch 5. A 5 base indexing sequence (CCAAC) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph20

text: Danio rerio

text: mixed


text: Larval - day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: ZMP_phenotype_20_5_sibling-sc-2013-04-11T15:21:17Z-1610782

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from morphologically normal sibling embryos from ZMP phenotype 20 clutch 5. A 5 base indexing sequence (AGCGC) is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph20

text: Danio rerio

text: mixed


text: Human

text: Promega

characteristic: External Id

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:18:57Z-1607055

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

characteristic: INSDC center name

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:03Z-1607061

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

characteristic: INSDC first public

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:06Z-1607064

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:09Z-1607067

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:15Z-1607073

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:18Z-1607076

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:21Z-1607079

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:24Z-1607082

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:27Z-1607085

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:30Z-1607088

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:33Z-1607091

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:36Z-1607094

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:39Z-1607097

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:42Z-1607100

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:46Z-1607103

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:49Z-1607106

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Human

text: Promega

text: SC

text: public

text: Homo_sapiens-sc-2013-04-03T15:19:53Z-1607109

text: human

text: Homo sapiens

text: genomic DNA

text: Homo sapiens

text: Promega


text: Institut de la Recherche Agronomique

text: public

characteristic: biological replicate

text: ArrayExpress

characteristic: broker name

text: granulosa cell

characteristic: cell type

text: sheep

text: Protocols: Laser Capture Microdissection from Transcriptome profiling of sheep granulosa cells and oocytes during early follicular development obtained by Laser Capture Microdissection Bonnet et al 2010 (doi: 10.1186/1471-2164-12-417) RNA extraction from Transcriptome profiling of sheep granulosa cells and oocytes during early follicular development obtained by Laser Capture Microdissection Bonnet et al 2010 (doi: 10.1186/1471-2164-12-417) T7 linear amplification from Transcriptome profiling of sheep granulosa cells and oocytes during early follicular development obtained by Laser Capture Microdissection Bonnet et al 2010 (doi: 10.1186/1471-2164-12-417) All RNAseq libraries were constructed from 200 ng of aRNA using Illumina TruSeq RNA Sample Prep (Illumina, San Diego, CA USA) following manufacturers instruction. Each biological replicate was identified by a different index. Libraries were quantified using QPCR NGS Library Quant Kit (Agilent). Three libraries were pooled and loaded randomly per lane at 8 pM concentration.

characteristic: description

text: secondary follicle

characteristic: developmental stage

text: Ovis aries

text: Ovis aries

text: ovary

characteristic: organism part

text: Ovis aries

text: female

characteristic: sex

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


text: EMBL European Bioinformatics Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:EMBL European Bioinformatics Institute

characteristic: Submitter Id

text: 2 week

characteristic: age

text: ArrayExpress

text: Japanese rice

text: Nipponbare

characteristic: cultivar

text: Protocols: Oryza sativa L. japonica nipponbare seedlings were grown in growth chambers to the 2-3 leaf stage. At 2 weeks old, they were subjected to salt stress treatment by watering with 300 mM NaCl solution (or normal watering for control plants). Treatment was applied at 10:00 PST (2 hours post-dawn). Seedling shoots (stem and leaves) were sampled at 1 hour, 5 hours, and 24 hours post-treatment. Total cellular RNA was extracted using RNA Plant Reagent (Life Technologies) and treated with RNase-free Turbo DNase (Life Technologies) followed by a clean-up step using Plant RNeasy kits (Qiagen). Concentration, integrity and extent of contamination by ribosomal RNA were assessed using ND-1000 spectrophotometer (Thermo Fisher Scientific) and Bioanalyzer 2100 (Agilent Technologies). For details see Fox et al. (2009) Applications for Ultra-high-Throughput Sequencing. In: Belostotsky (ed.), Plant Systems Biology, vol. 553, pp. 79--108. Libraries were prepared using the TruSeq(TM) RNA Sample Preparation Kits (v2).

text: seedling, two leaves visible, three leaves visible

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: shoot axis, vascular leaf

text: Oryza sativa Japonica Group


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CNRS

characteristic: INSDC center name

text: public

text: ArrayExpress

text: yellow fever mosquito

characteristic: common name

text: Protocols: Mosquitoes were reared in standard insectary conditions (26C, 14h/10h light/dark, 80% relative humidity) in tap water (larvae) and net cages (adults). Larvae and adults were fed with hay pellets and papers impregnated with honey respectively. Blood feeding of adult females was performed on mice. The laboratory strain Bora-Bora, originating from French Polynesia and fully susceptible to insecticides, was used as a parental strain to select different strains with the pyrethroid insecticide permethrin (Perm-R strain), the neonicotinoid insecticide imidacloprid (Imida-R strain), the carbamate insecticide propoxur (Propo-R strain) and Bacillus turingiensis toxins (LiTOX_N and LiTOX_S strains). For Perm-R, Imida-R and Propo-R strains, insecticide selection was performed by exposing early 4th-stage larvae for 24h to a lethal dose of each insecticide. For each strain, dose of insecticide was adjusted at each generation to reach 60-80% larval mortality after 24h exposure. Surviving larvae were transferred in clean tap water, fed with standard larval food and allowed to emerge. Adults were allowed to reproduce for 4-days and blood fed to obtain eggs for the next generation. In order to limit bottleneck effects, each generation was seeded with more than 6000 individuals. Selection process was carried out in parallel for all strains during 10 generations. During this process, the parental Bora-Bora strain was maintained in similar condition without insecticide selection. For LiTOX_N and LiTOX_S strains, selection as described in Paris et al. 2011 (DOI 10.1007/s10646-011-0663-8). For each strain, total RNA was extracted from G11 larvae not exposed to insecticides of three different egg batches. Each biological replicate consisted of 200 larvae reared in 200 mL tap water in standardized conditions. For each biological replicate, total RNA was extracted from 60 fourth-stage larvae using the RNAqueous-4PCR Kit (Applied Biosystems/Ambion, Austin, TX, USA), according to manufacturers instructions. Total RNA quality and quantity were assessed with a Nanodrop ND11000 (Thermo Scientific, USA) and a 2100 Bioanalyzer (Agilent, USA). After extraction, total RNAs from each biological replicate were pooled in equal quantity to obtain a total RNA mixture representative of 180 individuals. Total RNA pools from each strain were then used for preparing cDNA libraries using the mRNA-Seq Sample Prep Kit (Part 1004898 Rev D, Illumina, USA) according to manufacturers instructions. Two replicates of cDNA libraries were prepared for each strain

text: larval stage

text: Aedes aegypti

characteristic: organism

text: Aedes aegypti

text: Permethrin resistant

characteristic: phenotype

text: Aedes aegypti

text: fresh specimen

text: Perm-R

characteristic: strain

text: Perm-R


text: CNRS

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: yellow fever mosquito

characteristic: description

text: larval stage

characteristic: developmental stage

text: Aedes aegypti

text: Aedes aegypti

text: carbamate insecticide propoxur resistant

text: Aedes aegypti

text: fresh specimen

text: Propo-R

text: Propo-R


text: CNRS

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: yellow fever mosquito

text: larval stage

text: Aedes aegypti

text: Aedes aegypti

text: insecticide susceptible

text: Aedes aegypti

text: fresh specimen

characteristic: specimen with known storage state

text: Bora-Bora

text: Bora

characteristic: title


text: CNRS

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: yellow fever mosquito

text: larval stage

text: Aedes aegypti

text: Aedes aegypti

text: Bti resistant normal

text: Aedes aegypti

text: fresh specimen


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: CNRS

text: public

text: ArrayExpress

text: yellow fever mosquito

text: larval stage

text: Aedes aegypti

text: Aedes aegypti

text: Imidacloprid resistant

text: Aedes aegypti

text: fresh specimen

text: Imida-R

text: Imida-R


characteristic: External Id

text: CNRS

characteristic: INSDC center name

text: public

text: ArrayExpress

text: yellow fever mosquito

text: larval stage

text: Aedes aegypti

text: Aedes aegypti

text: Bti resistant slow development

text: Aedes aegypti

text: fresh specimen


text: University of Helsinki

text: public

tag: Namespace:University of Helsinki

text: ArrayExpress

characteristic: cell line

text: fruit fly

characteristic: common name

text: Protocols: Chromatin immunoprecipitation (ChIP)-assays were done as in Tuupanen et al.Nature Genetics 41, 885, 2009. ChIP-seq was performed essentially as described in (Tuupanen et al.Nature Genetics 41, 885, 2009) with the following modifications. ChIP for Myc and Max: S2 cells were formaldehyde crosslinked, sonicated and immunoprecipitated with the following set of antibodies (Santa Cruz Biotechnology, Inc.): Myc: dN-20 and d1-717, sc-15832 and sc-28207. Max: d1-160, sc-28209. IgG controls sc-2027 and sc-2028. ChIP for E2f and Myb: S2 cells were transiently transfected with plasmids (backbone pRmHa-1) containing metallothionein promoter driven Cterminally His-streptavidin binding peptide-3xV5 tagged Drosophila open reading frames. Expression of the genes was induced 24 hr after transfection by 0.5 mM CuSO4, and the incubation continued for 48 hr until formaldehyde crosslinking was done. Immunoprecipitations were made with 7.5 mg of monoclonal anti-V5 antibody (46-1157; Invitrogen) or IgG control antibody (sc-2025; Santa Cruz Biotechnology, Inc.) Chromatin immunoprecipitation (ChIP)-seq libraries were prepaired as in Tuupanen et al.Nature Genetics 41, 885, 2009. Library preparations were done by repairing the immunoprecipitated DNA using Klenow and T4 DNA polymerase and T4 polynucleotide kinase (MBI Fermentas, Vilnius, Latvia), and ligating the Illumina sequencing adapters according to manufacturers instructions.

text: transfection

characteristic: genetic modification

text: transfected with V5 tagged Myb ORF

characteristic: genotype

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Drosophila melanogaster

text: fresh specimen


text: University of Helsinki

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: description

text: transfection

text: transfected with V5 tagged E2f ORF

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: fresh specimen


text: ES Cells

characteristic: ArrayExpress-CellType

text: NanogGFP

characteristic: ArrayExpress-Genotype

text: male

characteristic: ArrayExpress-Sex

text: Mus Musculus

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: BSSeq from ESCs

characteristic: sample description

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL-EBI

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: baker's yeast

text: Protocols: This laboratory strain was derived from S. cerevisiae DBVPG 1014 . Cells were grown in YPD liquid medium for genomic DNA extraction DNA was extracted from 10^9 pelleted cells with the Qiagen Genomic DNA Isolation Kit following the manufacturer's instructions.

text: laboratory strain

characteristic: environmental history

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: frozen sample

characteristic: specimen with known storage state

characteristic: strain

characteristic: title


text: EMBL-EBI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: baker's yeast

characteristic: common name

text: Protocols: Human feces were plated on YPD (yeast extract 1%, peptone 2%, D-Glucose 2%) agar plates added with antibiotics to prevent bacterial growth. Yeast colonies were then collected and species was assessed by ITS1-4 sequencing. Cells were grown in YPD liquid medium for genomic DNA extraction DNA was extracted from 10^9 pelleted cells with the Qiagen Genomic DNA Isolation Kit following the manufacturer's instructions.

characteristic: description

text: clinical strain

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: frozen sample


text: EMBL-EBI

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: baker's yeast

text: Protocols: San Giovese Chianti Grape, Marchi and Cavalieri, 2008 (PMID: 19037676) Cells were grown in YPD liquid medium for genomic DNA extraction DNA was extracted from 10^9 pelleted cells with the Qiagen Genomic DNA Isolation Kit following the manufacturer's instructions.

text: environmental strain

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: frozen sample


characteristic: ENA-FIRST-PUBLIC

text: EMBL-EBI

text: public

text: ArrayExpress

text: baker's yeast

text: Protocols: San Giovese industrial fermentation, Marchi and Cavalieri, 2008 (PMID: 19037676) Cells were grown in YPD liquid medium for genomic DNA extraction DNA was extracted from 10^9 pelleted cells with the Qiagen Genomic DNA Isolation Kit following the manufacturer's instructions.

text: environmental strain

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: frozen sample


characteristic: ENA-LAST-UPDATE

text: University of Helsinki

text: public

text: ArrayExpress

characteristic: cell line

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: fresh specimen


characteristic: External Id

text: University of Helsinki

text: public

characteristic: SRA accession

text: ArrayExpress

text: fruit fly

text: transfection

characteristic: genetic modification

text: transfected with Myc tagged E2f ORF

characteristic: genotype

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: fresh specimen


text: University of Helsinki

text: public

text: E-MTAB-1648:s_7_sequence.txt.E2f_IgG_MG132

characteristic: Submitter Id

text: ArrayExpress

text: fruit fly

text: transfection

text: transfected with V5 tagged E2f ORF

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: fresh specimen

characteristic: specimen with known storage state


text: EMBL-EBI

characteristic: INSDC center name

text: public

text: ArrayExpress

text: baker's yeast

text: Protocols: Vespa crabro gut isolated strain, Stefanini et al., 2012 (PMID:22847440) Cells were grown in YPD liquid medium for genomic DNA extraction DNA was extracted from 10^9 pelleted cells with the Qiagen Genomic DNA Isolation Kit following the manufacturer's instructions.

text: clinical strain

characteristic: environmental history

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: frozen sample

characteristic: strain

characteristic: title


text: EMBL-EBI

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: baker's yeast

characteristic: common name

characteristic: description

text: environmental strain

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: frozen sample


characteristic: ENA-FIRST-PUBLIC

text: EMBL-EBI

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: baker's yeast

text: Protocols: The content of a Vespa crabro gut was plated on YPD (yeast extract 1%, peptone 2%, D-Glucose 2%) agar plates added with antibiotics to prevent bacterial growth. Yeast colonies were then collected and species was assessed by ITS1-4 sequencing. Cells were grown in YPD liquid medium for genomic DNA extraction DNA was extracted from 10^9 pelleted cells with the Qiagen Genomic DNA Isolation Kit following the manufacturer's instructions.

text: environmental strain

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: frozen sample


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Helsinki

text: public

characteristic: SRA accession

text: ArrayExpress

characteristic: cell line

text: fruit fly

text: transfection

text: transfected with HA tagged E2f ORF

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: fresh specimen


text: University of Helsinki

text: public

characteristic: Submitter Id

text: ArrayExpress

text: fruit fly

text: transfection

characteristic: genetic modification

text: transfected with HA tagged Myb ORF

characteristic: genotype

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: fresh specimen

characteristic: specimen with known storage state


text: University of Helsinki

characteristic: INSDC center name

text: public

text: ArrayExpress

text: fruit fly

text: transfection

text: transfected with Myc tagged Myb ORF

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: fresh specimen

characteristic: title


text: Plasmodium falciparum

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC first public

text: public

text: Pf_TM180_L-sc-2013-04-18T11:56:12Z-1613443

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: EMBL-EBI

text: public

text: ArrayExpress

characteristic: broker name

text: baker's yeast

characteristic: common name

text: Protocols: Strain isolated from rotten fig, Mortimer and Johnston, 1986 Cells were grown in YPD liquid medium for genomic DNA extraction DNA was extracted from 10^9 pelleted cells with the Qiagen Genomic DNA Isolation Kit following the manufacturer's instructions.

characteristic: description

text: environmental strain

characteristic: environmental history

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: frozen sample

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMBL-EBI

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: baker's yeast

text: Protocols: Montalcino Grape, Cavalieri et al 2000 (PMID: 11035792). Cells were grown in YPD liquid medium for genomic DNA extraction DNA was extracted from 10 raise to 9 pelleted cells with the Qiagen Genomic DNA Isolation Kit following the manufacturer's instructions. Libraries were constructed using Illumina TruSeq DNA Sample Prep standard protocol. Briefly, 5 ug of high molecular weight genomic DNA (gDNA) was fragmented by Covaris sonication device. Following sonication, DNA fragments were end-repaired and A-tailed. Adapters were then ligated via a 3 prime thymine overhang. Finally, ligated fragments were amplified by PCR (10 cycles). insert sizes were about 400-500 bp as evaluated in an Agilent DNA 1000 Analyzer Chip.

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: frozen specimen


prosim

characteristic: ENA-CHECKLIST

text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

characteristic: External Id

text: ILM

text: public

characteristic: SRA accession

text: prosim

characteristic: Submitter Id

text: greater bamboo lemur

text: Prolemur simus

text: Prolemur simus

text: HSI


sapxan

text: SRA-Webin

text: ILM

characteristic: INSDC center name

text: public

text: sapxan

text: yellow-breasted capuchin

text: Sapajus xanthosternos

text: Sapajus xanthosternos

characteristic: title


thegel

text: SRA-Webin

text: ILM

characteristic: INSDC first public

text: public

text: thegel

text: gelada

text: Theropithecus gelada

text: Theropithecus gelada