text: SRA-Webin

text: MMRI

text: public

text: human

text: RC-seq colon cancer tumor 10 lane 2

characteristic: description

text: Homo sapiens

text: Homo sapiens


status: PUBLIC

tag: attribute

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

characteristic: External Id

text: MMRI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: human

characteristic: common name

text: RC-seq colon cancer tumor 4 lane 2

text: Homo sapiens

characteristic: organism

text: Homo sapiens

characteristic: title

type: has member


text: SRA-Webin

text: MMRI

text: public

text: human

text: RC-seq colon cancer control 6 lane 1

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: MMRI

text: public

text: human

text: RC-seq colon cancer tumor 10 lane 1

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: MMRI

text: public

text: human

text: RC-seq colon cancer control 4 lane 1

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: MMRI

text: public

text: human

text: RC-seq colon cancer control 1 lane 1

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: MMRI

text: public

text: human

text: RC-seq colon cancer tumor 8 lane 2

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: MMRI

text: public

text: human

text: RC-seq colon cancer control 1 lane 2

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: MMRI

text: public

text: human

text: RC-seq colon cancer control 10 lane 2

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: MMRI

text: public

text: human

text: RC-seq colon cancer control 8 lane 2

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: MMRI

text: public

text: human

text: RC-seq colon cancer control 8 lane 1

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: MMRI

text: public

text: human

text: RC-seq colon cancer tumor 8 lane 1

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: MMRI

text: public

text: human

text: RC-seq colon cancer control 4 lane 2

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: MMRI

text: public

text: human

text: RC-seq colon cancer control 6 lane 2

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: MMRI

text: public

text: human

text: RC-seq colon cancer tumor 1 lane 2

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: MMRI

text: public

text: human

text: RC-seq colon cancer tumor 4 lane 1

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: MMRI

text: public

text: human

text: RC-seq colon cancer tumor 1 lane 1

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: MMRI

text: public

text: human

text: RC-seq colon cancer control 10 lane 1

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: MMRI

text: public

text: human

text: RC-seq colon cancer tumor 6 lane 1

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: MMRI

text: public

text: human

text: RC-seq colon cancer tumor 6 lane 2

text: Homo sapiens

text: Homo sapiens


text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: MDDH13_2g-sc-2012-06-28T09:50:48Z-1443920

text: house mouse

text: Mus musculus

text: DNA from Tail

characteristic: sample description

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: MDDH13_2b-sc-2012-06-28T09:50:46Z-1443919

text: house mouse

text: Mus musculus

text: DNA from Tail

text: Mus musculus


text: male

text: Mus musculus

text: SC

text: public

text: MDDH13_2b-sc-2012-06-27T16:35:39Z-1443725

text: house mouse

text: Mus musculus

text: DNA from Tail

text: Mus musculus


text: female

text: Mus musculus

text: SC

text: public

text: MDDH13_2g-sc-2012-06-27T16:35:41Z-1443726

text: house mouse

text: Mus musculus

text: DNA from Tail

text: Mus musculus


E-MTAB-1294:Mouse pool 2

text: public

characteristic: StrainOrLine

text: E-MTAB-1294:Mouse pool 2

tag: Namespace:Hospital Clinic de Barcelona, IDIBAPS, CIBERDEM

text: 10 to 14 week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: All animal experiments were conducted as approved by the Ethical Committee of Animal Experimentation of our institutions and in accordance with national regulations. Islets were obtained from 10-14 week-old male C57BL/6J mice. For sequencing we obtained RNA from islets after culture at 37 degrees C in a humidified chamber with 5% CO2 for 72 hr in RPMI 1640 medium with 11 mM Glucose supplemented with 10% fetal calf serum, 100 U/ml penicillin, and 100 U/ml streptomycin.

characteristic: description

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

characteristic: sex

text: Mouse pool 2


E-MTAB-1294:HI 21

text: No

characteristic: ClinicalInformation: Premortem diagnosis of diabetes

text: 9.5 millimolar

characteristic: ClinicalInformation: Premortem non-fasting glycemia

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Hospital Clinic de Barcelona, IDIBAPS, CIBERDEM

characteristic: INSDC center name

text: public

text: E-MTAB-1294:HI 21

text: 70 year

characteristic: bmi

text: ArrayExpress

text: cause of death: cerebral hemorrage

characteristic: clinical history

text: human

text: Protocols: All experiments were performed according to protocols approved by the Institutional ethical committees of the Hospital Clinic de Barcelona, Geneva University Hospitals, Istituto Scientifico Ospedale San Raffaele, Oxford University, UK Human Tissue Authority and University of Lille. Samples were isolated from multiorgan donors without a history of glucose intolerance after informed consent from family members. Donor variables and cold ischemia times of the samples used in this study are provided separately. Pancreatic islets were isolated and purified according to established isolation procedures. After isolation, islets were incubated at 37 degrees C in a humidified chamber with 5% CO2 in CMRL 1066 medium with 10% fetal calf serum for various periods prior to shipment at room temperature in the same culture medium. Upon arrival, islets were re-cultured at 37 degrees C in a humidified chamber with 5% CO2 in RPMI 1640 medium supplemented with 10% fetal calf serum, 100 U/ml penicillin, and 100 U/ml streptomycin for three days before extraction of RNA or chromatin. Islet purity was assessed by dithizone staining using an aliquot of islets immediately prior to harvest. Further assessment of islet purity was carried out by qPCR analysis of duct, acinar, and beta-cell specific markers (SOX9, CPA1, MIST1, NKX6.1, and INS). Only samples showing marginal exocrine contaminant mRNAs were further processed. Acinar-enriched fractions were obtained after gradient purification of islets.

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: male

text: HI 21


E-MTAB-1294:HI 10

text: No

text: 6.9 millimolar

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-1294:HI 10

characteristic: Submitter Id

text: 53 year

text: ArrayExpress

text: cause of death: cerebral hemorrage

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: male

text: HI 10

characteristic: title


E-MTAB-1294:HI 33

text: No

text: NA millimolar

text: public

text: E-MTAB-1294:HI 33

text: 31 year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: cause of death: cerebral anoxia

text: human

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: male

characteristic: sex

text: HI 33


E-MTAB-1294:Mouse pool1

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: StrainOrLine

text: E-MTAB-1294:Mouse pool1

text: 10 to 14 week

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

text: Mouse pool1


E-MTAB-1294:Acinar tissue donor

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-1294:Acinar tissue donor

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Acinar tissue donor


E-MTAB-1294:HI E1

text: No

characteristic: ClinicalInformation: Premortem diagnosis of diabetes

text: NA millimolar

characteristic: ClinicalInformation: Premortem non-fasting glycemia

characteristic: INSDC first public

text: public

text: E-MTAB-1294:HI E1

text: 59 year

characteristic: bmi

text: ArrayExpress

text: human

text: Protocols: All experiments were performed according to protocols approved by the Institutional ethical committees of the Hospital Clinic de Barcelona, Geneva University Hospitals, Istituto Scientifico Ospedale San Raffaele, Oxford University, UK Human Tissue Authority and University of Lille. Samples were isolated from multiorgan donors without a history of glucose intolerance after informed consent from family members. Donor variables and cold ischemia times of the samples used in this study are provided separately. Pancreatic islets were isolated and purified according to established isolation procedures. After isolation, islets were incubated at 37 degrees C in a humidified chamber with 5% CO2 in CMRL 1066 medium with 10% fetal calf serum for various periods prior to shipment at room temperature in the same culture medium. Upon arrival, islets were re-cultured at 37 degrees C in a humidified chamber with 5% CO2 in RPMI 1640 medium supplemented with 10% fetal calf serum, 100 U/ml penicillin, and 100 U/ml streptomycin for three days before extraction of RNA or chromatin. Islet purity was assessed by dithizone staining using an aliquot of islets immediately prior to harvest. Further assessment of islet purity was carried out by qPCR analysis of duct, acinar, and beta-cell specific markers (SOX9, CPA1, MIST1, NKX6.1, and INS). Only samples showing marginal exocrine contaminant mRNAs were further processed. Acinar-enriched fractions were obtained after gradient purification of islets. Human beta-cells were further purified from isolated islets by Fluorescence Activated Cell Sorting using the zinc dye Newport Green and exclusion of duct and dead cells. beta-cell purity was ascertained by immunofluorescence, using polyclonal guinea pig anti-insulin antiserum (1:500), followed by texas red-conjugated goat anti-guinea pig antiserum (1:50, Vector Laboratories, Peterborough, UK) in conjunction with nuclear staining with DAPI (Vector Laboratories). Images were captured using a Zeiss LSM510 confocal laser scanning microscope (Carl Zeiss, Jena, Germany). Preparations with greater than 90% insulin-positive cells were used for sequencing.

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: male

text: HI E1


E-MTAB-1294:HI 25

text: No

text: 11.3 millimolar

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-1294:HI 25

characteristic: Submitter Id

text: 59 year

text: ArrayExpress

text: cause of death: ischemic brain injury

characteristic: clinical history

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: male

text: HI 25


E-MTAB-1294:HI 20

text: No

text: 9.4 millimolar

text: public

text: E-MTAB-1294:HI 20

text: 70 year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: cause of death: cerebral trauma

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: male

text: HI 20

characteristic: title


E-MTAB-1294:HI 34

text: No

text: 6.4 millimolar

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-1294:HI 34

text: 62 year

text: ArrayExpress

text: cause of death: cerebral trauma

text: human

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: male

characteristic: sex

text: HI 34


E-MTAB-1294:HI E2

text: No

characteristic: ClinicalInformation: Premortem diagnosis of diabetes

text: NA millimolar

characteristic: ClinicalInformation: Premortem non-fasting glycemia

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-1294:HI E2

text: 41 year

text: ArrayExpress

text: cause of death: meningioma

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: male

text: HI E2


E-MTAB-1294:HI 32

text: No

text: 5.1 millimolar

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-1294:HI 32

text: 38 year

characteristic: bmi

text: ArrayExpress

text: cause of death: trauma

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: male

text: HI 32


text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Eimeria tenella strain Houghton

text: Eimeria tenella strain Houghton

text: Houghton

characteristic: strain


text: Wellcome Trust Sanger Institute

text: public

tag: Namespace:Wellcome Trust Sanger Institute

text: frozen sample

characteristic: bio source type

text: Clontech

characteristic: biosourceprovider

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Protocols: Human polyA+ RNAs were purchased from Clontech. The RNAs were isolated from tissue samples using a modified guanidium thiocynate extraction method followed by polyA+ RNA selection with two rounds of oligo(dT)-cellulose columns. We experimentally assessed three categories of gene models: (1) spliced models in which one primer could be placed within 75 nt of a junction and that will result in about half of the sequencing reads covering the junction ('Multi-span'); (2) spliced models in which this was unfeasible ('Multi'); and (3) monoexonic genes ('Mono'). In the case of 'Multi-span' primers, the 'junction primer' is positioned within an exon not more than 65 bp away from the targeted junction to ensure that sequencing reads will cross the junctions with a minimum of 10 nt, while the second primer maps within an adjacent exon. To increase the fraction of junctions we could possibly test, we then designed primer pairs further away from the junction ('Multi' primers). Primers were designed using Primer3. We used parameters minimizing the formation of primer dimers and maximizing primers 'stickiness'. Primer pairs were further filtered for mapping within repeat-regions and alternative priming within 30 kb in duplications and paralogous sequences (maximum of two tolerated mismatches). First-strand cDNA samples were prepared from human poly(A)+ RNAs (BD-Clontech) with the SuperScript III kit (Invitrogen). Amplifications were performed in a final volume of 12.5 uL with JumpStart REDTaq ReadyMix (Sigma-Aldrich) and a primer concentration of 0.4 uM in 384-well plates format on an automatized Evoware platform (TECAN) combined with a Tetrad2 thermocycler (Bio-Rad) that allows processing four plates in parallel. Because monoexonic amplification is sensitive to genomic DNA contaminations, monoexonic models were assessed by amplification of cDNA in which a dNTP analog was incorporated using the mRNA Selective PCR Kit (TAKARA).

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: muscle

characteristic: organism part

text: Homo sapiens

text: male


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Wellcome Trust Sanger Institute

text: public

text: frozen sample

text: Clontech

text: ArrayExpress

text: human

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: spleen

text: Homo sapiens

text: mixed sex

characteristic: sex

characteristic: title


characteristic: External Id

text: Wellcome Trust Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: frozen sample

text: Clontech

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens

text: male


text: Wellcome Trust Sanger Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: frozen sample

text: Clontech

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens

text: male


text: Wellcome Trust Sanger Institute

text: public

text: frozen sample

characteristic: bio source type

text: Clontech

characteristic: biosourceprovider

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: heart

text: Homo sapiens

text: male


text: Wellcome Trust Sanger Institute

text: public

text: frozen sample

text: Clontech

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: testis

text: Homo sapiens

text: male


text: Wellcome Trust Sanger Institute

text: public

text: frozen sample

text: Clontech

text: ArrayExpress

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

text: mixed sex


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Wellcome Trust Sanger Institute

text: public

text: frozen sample

text: Clontech

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens

text: mixed sex


text: Plasmodium falciparum

characteristic: ArrayExpress-Species

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: Plasmodium falciparum

text: IT

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum

text: IT

characteristic: strain


text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Mus musculus

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: NODshiLtJ-sc-2012-08-09T16:36:16Z-1464791

text: house mouse

text: Mus musculus

text: Mus musculus


text: Danio rerio

text: TL/AB

text: SC

text: public

characteristic: SRA accession

text: SL4_06_B6-sc-2012-04-25T15:05:11Z-1404068

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: Exome

characteristic: sample description

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_C6-sc-2012-04-25T15:05:13Z-1404069

text: zebrafish

characteristic: common name

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_E5-sc-2012-04-25T15:05:07Z-1404063

text: zebrafish

text: Danio rerio

characteristic: organism

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_F5-sc-2012-04-25T15:05:08Z-1404064

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_B1-sc-2012-04-25T15:04:34Z-1404028

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_A1-sc-2012-04-25T15:04:33Z-1404027

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_G5-sc-2012-04-25T15:05:09Z-1404065

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_H5-sc-2012-04-25T15:05:10Z-1404066

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_A6-sc-2012-04-25T15:05:11Z-1404067

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_B5-sc-2012-04-25T15:05:04Z-1404060

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_C5-sc-2012-04-25T15:05:05Z-1404061

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_D5-sc-2012-04-25T15:05:06Z-1404062

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_C1-sc-2012-04-25T15:04:35Z-1404029

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_F1-sc-2012-04-25T15:04:38Z-1404032

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_G1-sc-2012-04-25T15:04:39Z-1404033

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_H1-sc-2012-04-25T15:04:40Z-1404034

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_A2-sc-2012-04-25T15:04:41Z-1404035

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_D1-sc-2012-04-25T15:04:36Z-1404030

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_B2-sc-2012-04-25T15:04:42Z-1404036

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_C2-sc-2012-04-25T15:04:43Z-1404037

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_E2-sc-2012-04-25T15:04:45Z-1404039

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_D2-sc-2012-04-25T15:04:44Z-1404038

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_H2-sc-2012-04-25T15:04:47Z-1404042

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_A3-sc-2012-04-25T15:04:48Z-1404043

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

text: SL4_06_G2-sc-2012-04-25T15:04:46Z-1404041

text: zebrafish

text: Danio rerio

text: Exome

text: Danio rerio

text: TL/AB


text: Danio rerio

text: TL/AB

text: SC

text: public

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text: Protocols: CyT49 (Viacyte proprietary male hESC line, normal karyotype) was grown as a monolayer culture by their standard methods [K. DÕAmour, personal communication]. Briefly, cells were thawed at 10 x 10^6 cells per T175 flask and grown in DMEM/F12 media (Gibco), 10% Xenofree Knockout Serum Replacement (Gibco), 1x non-essential amino acids (Gibco), 1% Glutamax (Gibco), 1% penicillin/streptomycin plus 10ng/ml activin A and Heregulin _1 at 37¡C and 8% CO2. Prior to initiating cellular differentiation, formation of cellular aggregates was achieved by placing the single cell suspension of undifferentiated ESCs into a rotational culture in 6-well, low attachment tissue culture plates in ESC growth media. Plates were rotated at 95 rpm overnight. For initiation of differentiation, the aggregates were pooled and washed with PBS prior to resuspending in day 0 differentiation media. Cells were treated with ActivinA + Wnt3a for one day, ActivinA alone for one day, KGF+ITS+TGF-Inhibitor for 3 days, Cyclopamine+TTNPB+Noggin for 3 days, KGF+EGF+Noggin for 3 days. Samples were taken at days 0, 1, 2, 5, 8 and 11 10 x 10^6 d0 cells and 3000 aggregates (d1-11) were fixed in 11% formaldehyde for ChIP-seq as described http://www.genpathway.com/support/fixation.html.

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