E-MTAB-6553:Sample 125

text: public

text: E-MTAB-6553:Sample 125

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: Adenoma

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

text: WT

text: WT

text: Sample 125

characteristic: tumor weight


E-MTAB-6553:Sample 136

status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6553:Sample 136

tag: Namespace:Institut Cochin, INSERM U1016, CNRS UMR 8104, Universite Paris Descartes, Sorbonne Paris Cite.

characteristic: Submitter Id

text: ArrayExpress

text: human

text: Protocols: Samples are snap frozen tissue in liquid nitrogen. All samples were stored at -80C. miRNA-Seq libraries are performed from at least 1µg of extracted total RNA with a RIN greater than 7. Before starting, total RNAs are purified with miRNeasy kit wich allows the selection of the small RNA fraction less than 100b. From these samples enriched in small RNAs, libraries are performed according to the protocol published by François Vigneault : Curr Protoc Hum Genet. 2012 Apr;Chapter 11:Unit 11.12.1-10. \High-throughput multiplex sequencing of miRNA\; Vigneault F, Ter-Ovanesyan D, Alon S, Eminaga S, C Christodoulou D, Seidman JG, Eisenberg E, M Church G. miRNA-Seq libraries are performed from at least 1ug of extracted total RNA with a RIN greater than 7. Before starting, total RNAs are purified with miRNeasy kit wich allows the selection of the small RNA fraction less than 100b. From these samples enriched in small RNAs, libraries are performed according to the protocol published by François Vigneault : Curr Protoc Hum Genet. 2012 Apr;Chapter 11:Unit 11.12.1-10. High-throughput multiplex sequencing of miRNA; Vigneault F, Ter-Ovanesyan D, Alon S, Eminaga S, C Christodoulou D, Seidman JG, Eisenberg E, M Church G. Extraction with Qiacube-miRNeasy 96 Mini (Qiagen) kits; 1 to 10 ug per sample, concentration in range 70-500 ng/uL, volume range 15 to 50 uL, BioAnalyzer profile RIN > 7; Ligation, amplification , quantification and purification according to manufacturer's instructions, with the following details: First, a 3 prime adenylated DNA adaptor is ligated to the enriched sample in the absence of ATP preventing the self-ligation of miRNAs.Then a 5 prime RNA adaptor is ligated in the presence of ATP at the other end of the miRNAs.The RT primer complementary of the 3 prime adaptor is added at this stage with which it will form a duplex thereby reducing the ligation between adaptors. A reverse transcription is therefore perfomed from the RT primer and finally these captured miRNAs are amplified by PCR with primers complementary to the 3 prime and 5 prime adaptors. During this PCR a specific barcode is incorporated allowing individualisation of each library.Each PCR is loaded on the Fragment Analyzer (AATI) for a precise quantification of each miRNA peak of interest.Based on these results a equimolar pool of about ten of different samples are performed. Finally the pooled PCR product is loaded on PAGE in order to excise the band of miRNA that is extracted and purified on a Qiagen MinElute column. Pool Concentration between 0.97 and 4.84 nM per uL; purification quantity is 3500 ng

text: Adenoma

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: adrenal cortex

characteristic: organism part

text: Homo sapiens

text: Subclinical

characteristic: secretion

text: female

characteristic: sex

text: Sample 136

characteristic: title

unit: centimeter

characteristic: tumor size

unit: gram


E-MTAB-6553:Sample 140

text: Institut Cochin, INSERM U1016, CNRS UMR 8104, Universite Paris Descartes, Sorbonne Paris Cite.

text: public

text: E-MTAB-6553:Sample 140

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: Adenoma

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

text: Sample 140

characteristic: tumor weight


E-MTAB-6553:Sample 29

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-6553:Sample 29

text: ArrayExpress

text: human

text: Primary Macronodular Hyperplasia

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

text: WT

text: WT

text: Sample 29


E-MTAB-6553:Sample 144

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6553:Sample 144

characteristic: Submitter Id

text: ArrayExpress

text: human

text: Primary Macronodular Hyperplasia

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

text: Mutated

text: Sample 144


E-MTAB-6553:Sample 37

text: public

text: E-MTAB-6553:Sample 37

text: ArrayExpress

text: human

text: Primary Macronodular Hyperplasia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: adrenal cortex

characteristic: organism part

text: Homo sapiens

text: Cushing

characteristic: secretion

text: female

characteristic: sex

text: WT

text: WT

text: Sample 37

characteristic: title


E-MTAB-6553:Sample 58

text: public

text: E-MTAB-6553:Sample 58

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: Primary Macronodular Hyperplasia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

text: WT

text: Sample 58


E-MTAB-6553:Sample 59

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-6553:Sample 59

text: ArrayExpress

text: human

text: Primary Macronodular Hyperplasia

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: male

text: Mutated

text: Sample 59

characteristic: tumor weight


E-MTAB-6553:Sample 109

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6553:Sample 109

text: ArrayExpress

text: human

text: Primary Macronodular Hyperplasia

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

text: WT

text: Sample 109


E-MTAB-6553:Sample 128

text: public

text: E-MTAB-6553:Sample 128

characteristic: Submitter Id

text: ArrayExpress

text: human

text: Primary Macronodular Hyperplasia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: adrenal cortex

characteristic: organism part

text: Homo sapiens

text: Cushing

characteristic: secretion

text: male

characteristic: sex

text: WT

text: Sample 128


E-MTAB-6553:Sample 134

text: public

text: E-MTAB-6553:Sample 134

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: Primary Macronodular Hyperplasia

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

text: WT

text: Sample 134

characteristic: title


E-MTAB-6553:Sample 142

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-6553:Sample 142

text: ArrayExpress

text: human

text: Primary Macronodular Hyperplasia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Subclinical

text: female

text: Mutated

text: Sample 142


E-MTAB-6553:Sample 143

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-6553:Sample 143

text: ArrayExpress

text: human

text: Primary Macronodular Hyperplasia

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

text: WT

text: WT

text: Sample 143


E-MTAB-6553:Sample 120

text: public

characteristic: SRA accession

text: E-MTAB-6553:Sample 120

characteristic: Submitter Id

text: ArrayExpress

text: human

text: Primary Macronodular Hyperplasia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: adrenal cortex

characteristic: organism part

text: Homo sapiens

text: Cushing

text: female

text: WT

text: WT

text: Sample 120

characteristic: tumor size

characteristic: tumor weight


E-MTAB-6553:Sample 19

text: public

text: E-MTAB-6553:Sample 19

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: Primary Macronodular Hyperplasia

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

characteristic: secretion

text: female

characteristic: sex

text: Mutated

text: WT

text: Sample 19


E-MTAB-6553:Sample 17

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-6553:Sample 17

text: ArrayExpress

text: human

text: Primary Macronodular Hyperplasia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

text: Mutated

text: WT

text: Sample 17

characteristic: title


E-MTAB-6553:Sample 11

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6553:Sample 11

characteristic: Submitter Id

text: ArrayExpress

text: human

text: Primary Macronodular Hyperplasia

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: male

text: WT

text: WT

text: Sample 11


E-MTAB-6553:Sample 50

text: public

text: E-MTAB-6553:Sample 50

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

text: Primary Macronodular Hyperplasia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: adrenal cortex

characteristic: organism part

text: Homo sapiens

text: Cushing

text: female

text: Mutated

text: Sample 50

characteristic: tumor weight


E-MTAB-6553:Sample 4

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-6553:Sample 4

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: Primary Macronodular Hyperplasia

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Non-secreting

characteristic: secretion

text: male

characteristic: sex

text: WT

text: WT

text: Sample 4


E-MTAB-6553:Sample 119

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-6553:Sample 119

text: ArrayExpress

text: human

text: Primary Macronodular Hyperplasia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: male

text: WT

text: WT

text: Sample 119

characteristic: title

characteristic: tumor size


E-MTAB-6553:Sample 126

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6553:Sample 126

characteristic: Submitter Id

text: ArrayExpress

text: human

text: Primary Macronodular Hyperplasia

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: male

text: WT

text: WT

text: Sample 126


E-MTAB-6553:Sample 129

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-6553:Sample 129

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

text: Primary Macronodular Hyperplasia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: adrenal cortex

characteristic: organism part

text: Homo sapiens

text: Cushing

text: female

text: Mutated

text: Sample 129

characteristic: tumor weight


E-MTAB-6553:Sample 64

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-6553:Sample 64

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: Primary Macronodular Hyperplasia

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

characteristic: secretion

text: female

characteristic: sex

text: Mutated

text: Sample 64


E-MTAB-6553:Sample 3

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-6553:Sample 3

text: ArrayExpress

text: human

text: Mineralocorticoid

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

text: Sample 3

characteristic: title


E-MTAB-6553:Sample 46

characteristic: ENA-CHECKLIST

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6553:Sample 46

characteristic: Submitter Id

text: ArrayExpress

text: human

text: Mineralocorticoid

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

text: Sample 46


E-MTAB-6553:Sample 56

text: public

text: E-MTAB-6553:Sample 56

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

text: Mineralocorticoid

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: adrenal cortex

characteristic: organism part

text: Homo sapiens

text: Cushing

text: female

text: Sample 56

characteristic: tumor weight


E-MTAB-6553:Sample 72

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-6553:Sample 72

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: Mineralocorticoid

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

characteristic: secretion

text: male

text: WT

text: WT

text: Sample 72


E-MTAB-6553:Sample 77

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-6553:Sample 77

text: ArrayExpress

text: human

text: Mineralocorticoid

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

characteristic: sex

text: Sample 77


E-MTAB-6553:Sample 79

characteristic: ENA-CHECKLIST

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6553:Sample 79

text: ArrayExpress

text: human

text: Mineralocorticoid

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

text: Sample 79

characteristic: title


E-MTAB-6553:Sample 83

text: public

text: E-MTAB-6553:Sample 83

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

text: Mineralocorticoid

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: adrenal cortex

characteristic: organism part

text: Homo sapiens

text: Cushing

text: male

text: Sample 83


E-MTAB-6553:Sample 87

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-6553:Sample 87

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: Mineralocorticoid

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

text: Sample 87

characteristic: tumor weight


E-MTAB-6553:Sample 89

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-6553:Sample 89

text: ArrayExpress

text: human

text: Mineralocorticoid

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

characteristic: secretion

text: male

text: Sample 89


E-MTAB-6553:Sample 93

characteristic: ENA-CHECKLIST

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6553:Sample 93

text: ArrayExpress

text: human

text: Mineralocorticoid

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

characteristic: sex

text: Sample 93

characteristic: tumor size


E-MTAB-6553:Sample 138

text: public

text: E-MTAB-6553:Sample 138

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

text: Mineralocorticoid

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: adrenal cortex

characteristic: organism part

text: Homo sapiens

text: Cushing

text: female

text: Sample 138

characteristic: title


E-MTAB-6553:Sample 9

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-6553:Sample 9

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: Mineralocorticoid

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

text: Sample 9

characteristic: tumor weight


E-MTAB-6553:Sample 24

characteristic: ENA-CHECKLIST

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6553:Sample 24

text: ArrayExpress

text: human

text: Mineralocorticoid

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

characteristic: secretion

text: Sample 24


E-MTAB-6553:Sample 60

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6553:Sample 60

characteristic: Submitter Id

text: ArrayExpress

text: human

text: Mineralocorticoid

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: Sample 60


E-MTAB-6553:Sample 66

text: public

text: E-MTAB-6553:Sample 66

text: ArrayExpress

characteristic: broker name

text: human

text: Mineralocorticoid

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: adrenal cortex

characteristic: organism part

text: Homo sapiens

text: Cushing

text: Sample 66


E-MTAB-6553:Sample 85

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-6553:Sample 85

text: ArrayExpress

text: human

text: Mineralocorticoid

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: Sample 85

characteristic: title


E-MTAB-6553:Sample 22

characteristic: External Id

text: public

text: E-MTAB-6553:Sample 22

characteristic: age

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: Mineralocorticoid

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: male

characteristic: sex

text: Sample 22

characteristic: tumor size


E-MTAB-6553:Sample 25

characteristic: ENA-CHECKLIST

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6553:Sample 25

text: ArrayExpress

text: human

text: Mineralocorticoid

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

text: Sample 25

characteristic: tumor weight


E-MTAB-6553:Sample 28

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6553:Sample 28

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: Mineralocorticoid

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

characteristic: secretion

text: female

text: Sample 28


E-MTAB-6553:Sample 31

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-6553:Sample 31

characteristic: age

text: ArrayExpress

text: human

text: Mineralocorticoid

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

characteristic: organism part

text: Homo sapiens

text: Cushing

text: female

text: Sample 31

characteristic: title


E-MTAB-6553:Sample 38

characteristic: ENA-CHECKLIST

characteristic: INSDC center name

text: public

text: E-MTAB-6553:Sample 38

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: Mineralocorticoid

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

characteristic: sex

text: Sample 38

characteristic: tumor size


E-MTAB-6553:Sample 42

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6553:Sample 42

text: ArrayExpress

text: human

text: Mineralocorticoid

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

text: Sample 42

characteristic: tumor weight


E-MTAB-6553:Sample 44

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-6553:Sample 44

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: Mineralocorticoid

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

characteristic: secretion

text: male

text: Sample 44


E-MTAB-6553:Sample 26

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-6553:Sample 26

characteristic: age

text: ArrayExpress

text: human

text: Primary Pigmented Micronodular Dysplasia

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

characteristic: organism part

text: Homo sapiens

text: Cushing

text: male

text: WT

text: Sample 26

characteristic: title


E-MTAB-6553:Sample 110

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6553:Sample 110

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

characteristic: sex

text: WT

text: Sample 110


E-MTAB-6553:Sample 30

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6553:Sample 30

text: ArrayExpress

text: human

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

text: Mutated

text: Sample 30

characteristic: tumor weight


characteristic: ENA-LAST-UPDATE

text: public

tag: Namespace:Max Planck Institute for Biogeochemistry

characteristic: Submitter Id

characteristic: collection date

text: tropical rainforest

characteristic: current vegetation

text: metagenome from Micrandropsis scleroxylon

text: tropical rainforest

characteristic: environment (biome)

text: plateau

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: Brazil

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenome

characteristic: organism

characteristic: ph

text: terpene soil

characteristic: project name

text: metagenome

text: Illumina HiSeq

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: Ferralsol

characteristic: soil taxonomic/fao classification

text: Metagenome from litter - L3


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Max Planck Institute for Biogeochemistry

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: tropical rainforest

characteristic: description

text: tropical rainforest

text: plateau

text: soil

text: Brazil

text: metagenome

text: metagenome

text: terpene soil

text: metagenome

text: Illumina HiSeq

text: soil

text: Ferralsol

text: Metagenome from from litter - L4

characteristic: title


text: public

text: tropical rainforest

characteristic: current vegetation

text: tropical rainforest

characteristic: environment (biome)

text: plateau

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: Brazil

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenome

characteristic: organism

characteristic: ph

text: terpene soil

characteristic: project name

text: metagenome

text: Illumina HiSeq

text: soil

text: Ferralsol

text: Metagenome from litter - L5


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: tropical rainforest

text: metagenome from soil

text: tropical rainforest

text: plateau

text: soil

text: Brazil

text: metagenome

text: metagenome

text: terpene soil

text: metagenome

text: Illumina HiSeq

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: Ferralsol

characteristic: soil taxonomic/fao classification

text: Metagenome from soil - S4


text: public

characteristic: collection date

text: tropical rainforest

characteristic: current vegetation

text: metagenome from soil

characteristic: description

text: tropical rainforest

characteristic: environment (biome)

text: plateau

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: Brazil

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenome

text: terpene soil

text: metagenome

text: Illumina HiSeq

text: soil

text: Ferralsol

text: Metagenome from soil - S5

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: tropical rainforest

text: metagenome from soil

text: tropical rainforest

text: plateau

text: soil

text: Brazil

text: metagenome

text: metagenome

characteristic: organism

characteristic: ph

text: terpene soil

characteristic: project name

text: metagenome

text: Illumina HiSeq

text: soil

text: Ferralsol

text: Metagenome from soil - S6M


text: public

characteristic: collection date

text: tropical rainforest

characteristic: current vegetation

text: metagenome from soil

characteristic: description

text: tropical rainforest

characteristic: environment (biome)

text: plateau

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: Brazil

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: metagenome

text: metagenome

text: terpene soil

text: metagenome

text: Illumina HiSeq

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: Ferralsol

characteristic: soil taxonomic/fao classification

text: Metagenome from soil - S3


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: tropical rainforest

text: metagenome from soil

text: tropical rainforest

text: plateau

text: soil

text: Brazil

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenome

text: terpene soil

text: metagenome

text: Illumina HiSeq

text: soil

text: Ferralsol

text: Metagenome from soil - S6

characteristic: title


E-MTAB-6553:Sample 65

text: public

text: E-MTAB-6553:Sample 65

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: adrenal cortex

characteristic: organism part

text: Homo sapiens

text: Cushing

characteristic: secretion

text: female

characteristic: sex

text: Sample 65

characteristic: tumor size

characteristic: tumor weight


E-MTAB-6553:Sample 80

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-6553:Sample 80

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

text: WT

text: WT

text: Sample 80


E-MTAB-6553:Sample 86

text: public

characteristic: SRA accession

text: E-MTAB-6553:Sample 86

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: female

text: WT

text: Sample 86

characteristic: title


E-MTAB-6553:Sample 95

text: public

text: E-MTAB-6553:Sample 95

text: ArrayExpress

text: human

characteristic: description

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: adrenal cortex

characteristic: organism part

text: Homo sapiens

text: Cushing

characteristic: secretion

text: female

characteristic: sex

text: WT

text: WT

text: Sample 95


E-MTAB-6553:Sample 96

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-6553:Sample 96

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: adrenal cortex

text: Homo sapiens

text: Cushing

text: male

text: WT

text: Sample 96


text: SLU

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: mitochondrion

characteristic: organelle

text: Plasmodiophora brassicae

text: Plasmodiophora brassicae

text: Plasmodiophora brassiere strain e3


text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: anonymized name

characteristic: collection date

text: Enterococcus faecalis

characteristic: common name

characteristic: culture collection

text: not available: to be reported later

characteristic: host status

text: not available: to be reported later

characteristic: isolation source

text: Enterococcus faecalis

text: Enterococcus faecalis

text: Lancefield Group D, serotype 20

characteristic: serovar

text: not available: to be reported later

characteristic: specific host

characteristic: strain


text: Homo sapien

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

characteristic: title


text: UNIVERSITY OF SZEGED

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:UNIVERSITY OF SZEGED

characteristic: Submitter Id

text: Herpes simplex virus type 1

text: PolyA selected mRNAs were isolated, reverse transcribed into cDNA and amplified by specific primers and sequencied usingPacBio Sequel platform

characteristic: description

text: Human alphaherpesvirus 1

text: Human alphaherpesvirus 1

text: Sequel PolyA


text: UNIVERSITY OF EXETER

text: public

tag: Namespace:UNIVERSITY OF EXETER

text: Construct of phage DMS3 carrying anti-crispr protein F1 initially isolated from phage JBD26 (recombined into DMS3)

text: Pseudomonas aeruginosa phage DMS3mVirAcrF4


text: UNIVERSITY OF COLOGNE

text: public

tag: Namespace:UNIVERSITY OF COLOGNE

text: not provided

characteristic: collection date

text: Germany, BB, Cottbus

characteristic: country

text: Acinetobacter pittii

text: Acinetobacter pittii


text: UNIVERSITY OF COLOGNE

text: public

text: not provided

text: Germany, NW, NRW

text: Acinetobacter pittii

text: Acinetobacter pittii


text: UNIVERSITY OF COLOGNE

text: public

text: not provided

text: Germany, BE, Berlin

text: Acinetobacter pittii

text: Acinetobacter pittii


text: UNIVERSITY OF COLOGNE

text: public

text: not provided

text: Germany, MV, Schwerin

text: Acinetobacter pittii

text: Acinetobacter pittii


text: Homo sapiens

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

characteristic: subject id


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COLOGNE

text: public

text: not provided

text: Germany, SN, SN

text: Acinetobacter pittii

text: Acinetobacter pittii


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COLOGNE

text: public

text: not provided

text: Germany, BW, BW

text: Acinetobacter pittii

text: Acinetobacter pittii


text: UNIVERSITY OF COLOGNE

text: public

text: not provided

text: Germany, BB, Berlin

text: Acinetobacter pittii

characteristic: organism

text: Acinetobacter pittii

characteristic: title


text: UNIVERSITY OF COLOGNE

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: not provided

text: Germany, NW, Leverkusen

text: Acinetobacter pittii

text: Acinetobacter pittii


text: UNIVERSITY OF COLOGNE

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: not provided

text: Germany, RP, Mainz

text: Acinetobacter pittii

text: Acinetobacter pittii


text: UNIVERSITY OF COLOGNE

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: Belgium, Belgium, Verviers

text: Acinetobacter pittii

text: Acinetobacter pittii


text: UNIVERSITY OF POTSDAM

text: public

tag: Namespace:UNIVERSITY OF POTSDAM

text: cave bear

text: Ursus spelaeus

text: Ursus spelaeus


text: SSI

text: public

text: ISS

characteristic: collected by

characteristic: collection date

text: Salmonella enterica

text: No

characteristic: environmental sample

text: Italy

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: Yes

characteristic: is the sequenced pathogen host associated?

characteristic: isolate

text: Salmonella enterica

text: Salmonella enterica

text: S. Typhimurium monophasic variant S. 4,[5],12:i:-

characteristic: serovar

text: monophasic Salmonella Typhimurium from Animals and Humans


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SSI

characteristic: INSDC center name

text: public

text: IZS

text: Salmonella enterica

characteristic: common name

text: No

text: Italy

text: not provided

text: Sus scrofa domesticus

text: Yes

text: Salmonella enterica

characteristic: organism

text: Salmonella enterica

characteristic: title


text: SSI

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ISS

characteristic: collected by

characteristic: collection date

text: Salmonella enterica

text: No

characteristic: environmental sample

text: Italy

text: not provided

text: Sus scrofa domesticus

text: Yes

text: Salmonella enterica

text: Salmonella enterica


text: Klebsiella pneumoniae

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

characteristic: subject id


text: Escherichia coli

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli


text: Pseudomonas aeruginosa

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: Acinetobacter baumannii

text: SC

characteristic: INSDC center name

text: public

text: Acinetobacter baumannii

characteristic: common name

text: Acinetobacter baumannii

text: Acinetobacter baumannii


text: UNIVERSITY OF COLOGNE

text: public

text: not provided

text: Germany, NW, Bochum

characteristic: country

text: Acinetobacter pittii

characteristic: organism

text: Acinetobacter pittii

characteristic: title


text: UNIVERSITY OF COLOGNE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: not provided

text: Turkey, NW, Bursa

text: Acinetobacter pittii

text: Acinetobacter pittii


text: UNIVERSITY OF COLOGNE

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: Belgium, Belgium, Brussels

text: Acinetobacter pittii

text: Acinetobacter pittii


text: UNIVERSITY OF POTSDAM

text: public

text: leopard

text: Panthera pardus

text: Panthera pardus


text: public

tag: Namespace:Clinical Pharmacology Department, William Harvey Research Institute, Queen Mary University London

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

text: house mouse

text: Protocols: 30 to 40 million ESCs or TSCs were fixed in 2 % formaldehyde (Agar Scientific) for 10 minutes at room temperature. Blastocyst-derived TS-EGFP cells were cultured under routine conditions (20% fetal bovine serum, 1 mM Na-pyruvate, Pen/Strep, 50 μM 2-mercaproethanol, 25 ng/ml bFGF and 1 μg/ml heparin in RPMI1640, with 70% of the medium pre-conditioned on embryonic feeder cells). J1 ESCs were grown in feeder-free conditions using DMEM-based medium with 15% FBS and 1,000 U/ml ESGRO LIF (Millipore). Hi-C libraries were prepared as described (Comoglio et al. 2018), with the ligation performed in nuclei (Nagano et al. 2015). Biotin-marked ligation products were isolated using MyOne Streptavidin C1 Dynabeads (Life Technologies), and the bead-bound Hi-C DNA was amplified with 7 PCR amplification cycles using PE PCR 1.0 and PE PCR 2.0 primers (Illumina). Promoter Capture Hi-C was performed as described (Schoenfelder et al. 2015a), using a custom-made RNA capture bait system (Agilent Technologies) consisting of 39,021 individual biotinylated RNAs targeting the ends of 22,225 promoter-containing mouse HindIII restriction fragments. The Hi-C library DNA (500 to 750 ng) was mixed with hybridization blockers (Agilent Technologies) and denatured for 5 minutes at 95˚C, then incubated with hybridization buffer and the RNA capture bait system at 65˚C for 24 hours (in a MJ Research PTC-200 PCR machine). After the hybridization incubation, DNA/biotin-RNA was isolated using MyOne Streptavidin T1 Dynabeads (Life Technologies), following the manufacturer’s instructions (SureSelect Target Enrichment, Agilent Technologies). After the final wash in wash buffer 2 (Agilent Technologies), the beads were resuspended in 300 µl NEBuffer 2 (NEB), isolated on a DynaMag-2 magnet (Life Technologies), and resuspended in a final volume of 30 µl NEBuffer 2. Hi-C libraries were prepared as described (Comoglio et al. 2018 doi/10.1101/gr.227272.117), with the ligation performed in nuclei (Nagano et al. 2015 doi.org/10.1186/s13059-015-0753-7). Biotin-marked ligation products were isolated using MyOne Streptavidin C1 Dynabeads (Life Technologies), and the bead-bound Hi-C DNA was amplified with 7 PCR amplification cycles using PE PCR 1.0 and PE PCR 2.0 primers (Illumina). Promoter Capture Hi-C was performed as described (Schoenfelder et al. 2015a doi/10.1101/gr.185272.114), using a custom-made RNA capture bait system (Agilent Technologies) consisting of 39,021 individual biotinylated RNAs targeting the ends of 22,225 promoter-containing mouse HindIII restriction fragments. The Hi-C library DNA (500 to 750 ng) was mixed with hybridization blockers (Agilent Technologies) and denatured for 5 minutes at 95˚C, then incubated with hybridization buffer and the RNA capture bait system at 65˚C for 24 hours (in a MJ Research PTC-200 PCR machine). After the hybridization incubation, DNA/biotin-RNA was isolated using MyOne Streptavidin T1 Dynabeads (Life Technologies), following the manufacturer’s instructions (SureSelect Target Enrichment, Agilent Technologies). After the final wash in wash buffer 2 (Agilent Technologies), the beads were resuspended in 300 µl NEBuffer 2 (NEB), isolated on a DynaMag-2 magnet (Life Technologies), and resuspended in a final volume of 30 µl NEBuffer 2. Following library enrichment, we performed PCR (four amplification cycles using Illumina PE PCR 1.0 and PE PCR 2.0 primers), and the Promoter CHi-C libraries were purified with AMPure XP beads (Beckman Coulter).

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: inner cell mass

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Clinical Pharmacology Department, William Harvey Research Institute, Queen Mary University London

characteristic: INSDC center name

text: public

text: ArrayExpress

text: embryonic stem cell

text: house mouse

characteristic: common name

text: embryo

text: normal

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: inner cell mass

text: Mus musculus

text: male


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: trophoblast stem cell

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: trophectoderm

text: Mus musculus

characteristic: title


text: UNIVERSITY OF POTSDAM

text: public

text: Gamssulzen cave bear

text: Ursus ingressus

text: Ursus ingressus


text: Mouse CD8 T cells

text: Isolated from spleen

text: male

characteristic: ArrayExpress-SEX

text: Mus musculus

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: house mouse

text: Male

characteristic: gender

text: Mus musculus

text: Mus musculus

characteristic: subject id


text: Mouse CD8 T cells

text: Isolated from spleen

text: female

text: Mus musculus

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

text: Female

text: Mus musculus

text: Mus musculus


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: WUR

text: public

text: EtBE reactor samples

characteristic: description

text: metagenome

text: metagenome

text: bacterial 16S rRNA


E-MTAB-6592:Sample 11

characteristic: INSDC center name

text: public

text: E-MTAB-6592:Sample 11

tag: Namespace:Karolinska Institutet, Department of Women's and Children's Health, Center for Molecular Medicine

unit: week

characteristic: age

text: ArrayExpress

text: human

characteristic: common name

text: Protocols: Embryonic and fetal bladders and genital tissue were obtained by surgeons from terminated pregnancies after informed consent and with ethics approval. Samples were taken from weeks 7 (n=2), 7,5 (n=1), 8 (n=3), 9 (n=4) for the bladder tissues and from weeks 7 (n=3), 8 (n=3), 9 (n=3) as well as 10 (n=4) for the genital tissues, respectively. Fresh tissues were dissected and immediately submerged in 5 volumes of RNAlater Stabilization Solution (Cat No. AM7020, Thermoisher Scientific, Waltham, MA), incubated at 4°C overnight and then transferred to -20°C. RNA was extracted by using TissueLyser LT (Cat No. 85600, QIAGEN, Hilden, Germany) and RNeasy Fibrous Tissue Mini Kit (cat. no. 74704, QIAGEN, Hilden, Germany). The RNA was measured both quantitatively and qualitatively using NanoDrop (Thermofisher Scientific, Waltham, MA) and Bioanalyzer 2100 (Agilent, Santa Clara, CA) instruments. Paired-end libraries of 2x126 bp with poly-A selection according to Illumina TruSeq Stranded mRNA protocol.

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: reproductive organ

characteristic: organism part

text: Homo sapiens

text: Sample 11


E-MTAB-6592:Sample 12

text: Karolinska Institutet, Department of Women's and Children's Health, Center for Molecular Medicine

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6592:Sample 12

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: embryo

text: normal

text: Homo sapiens

text: Homo sapiens

text: reproductive organ

text: Homo sapiens

text: Sample 12

characteristic: title


E-MTAB-6592:Sample 13

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-6592:Sample 13

text: ArrayExpress

text: human

text: embryo

text: normal

text: Homo sapiens

text: Homo sapiens

text: reproductive organ

text: Homo sapiens

text: Sample 13


E-MTAB-6592:Sample 14

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-6592:Sample 14

text: ArrayExpress

text: human

characteristic: description

text: embryo

text: normal

text: Homo sapiens

text: Homo sapiens

text: reproductive organ

text: Homo sapiens

text: Sample 14


E-MTAB-6592:Sample 15

text: public

text: E-MTAB-6592:Sample 15

characteristic: age

text: ArrayExpress

text: human

characteristic: common name

text: embryo

characteristic: developmental stage

text: normal

text: Homo sapiens

text: Homo sapiens

text: reproductive organ

text: Homo sapiens

text: Sample 15


E-MTAB-6592:Sample 16

text: public

text: E-MTAB-6592:Sample 16

text: ArrayExpress

text: human

text: embryo

text: normal

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: reproductive organ

characteristic: organism part

text: Homo sapiens

text: Sample 16


E-MTAB-6592:Sample 17

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-6592:Sample 17

text: ArrayExpress

text: human

text: late embryo

text: normal

text: Homo sapiens

text: Homo sapiens

text: reproductive organ

text: Homo sapiens

text: Sample 17


E-MTAB-6592:Sample 18

text: public

characteristic: SRA accession

text: E-MTAB-6592:Sample 18

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: late embryo

text: normal

text: Homo sapiens

text: Homo sapiens

text: reproductive organ

text: Homo sapiens

text: Sample 18


E-MTAB-6592:Sample 19

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-6592:Sample 19

text: ArrayExpress

text: human

text: late embryo

text: normal

text: Homo sapiens

text: Homo sapiens

text: reproductive organ

text: Homo sapiens

text: Sample 19

characteristic: title


E-MTAB-6592:Sample 20

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-6592:Sample 20

text: ArrayExpress

text: human

text: late embryo

text: normal

text: Homo sapiens

text: Homo sapiens

text: reproductive organ

text: Homo sapiens

text: Sample 20


E-MTAB-6592:Sample 21

text: public

text: E-MTAB-6592:Sample 21

characteristic: age

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: late embryo

text: normal

text: Homo sapiens

text: Homo sapiens

text: reproductive organ

text: Homo sapiens

text: Sample 21


E-MTAB-6592:Sample 22

text: public

text: E-MTAB-6592:Sample 22

text: ArrayExpress

text: human

text: late embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: reproductive organ

text: Homo sapiens

text: Sample 22


E-MTAB-6592:Sample 23

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6592:Sample 23

text: ArrayExpress

text: human

text: late embryo

text: normal

text: Homo sapiens

text: Homo sapiens

text: reproductive organ

characteristic: organism part

text: Homo sapiens

text: Sample 23


E-MTAB-6592:Sample 1

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6592:Sample 1

characteristic: Submitter Id

text: ArrayExpress

text: human

text: embryo

text: normal

text: Homo sapiens

text: Homo sapiens

text: urinary bladder

text: Homo sapiens

text: Sample 1


E-MTAB-6592:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-6592:Sample 2

text: 7 to 7.5

text: ArrayExpress

characteristic: broker name

text: human

text: embryo

text: normal

text: Homo sapiens

text: Homo sapiens

text: urinary bladder

text: Homo sapiens

text: Sample 2


E-MTAB-6592:Sample 3

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-6592:Sample 3

text: ArrayExpress

text: human

text: embryo

text: normal

text: Homo sapiens

text: Homo sapiens

text: urinary bladder

text: Homo sapiens

text: Sample 3

characteristic: title


E-MTAB-6592:Sample 4

characteristic: INSDC center name

text: public

text: E-MTAB-6592:Sample 4

characteristic: age

text: ArrayExpress

text: human

characteristic: common name

text: embryo

text: normal

text: Homo sapiens

text: Homo sapiens

text: urinary bladder

text: Homo sapiens

text: Sample 4


E-MTAB-6592:Sample 5

text: public

text: E-MTAB-6592:Sample 5

text: ArrayExpress

text: human

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: urinary bladder

text: Homo sapiens

text: Sample 5


E-MTAB-6592:Sample 6

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6592:Sample 6

text: ArrayExpress

text: human

text: embryo

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: urinary bladder

text: Homo sapiens

text: Sample 6


E-MTAB-6592:Sample 10

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6592:Sample 10

text: ArrayExpress

text: human

text: late embryo

text: normal

text: Homo sapiens

text: Homo sapiens

text: urinary bladder

characteristic: organism part

text: Homo sapiens

text: Sample 10


E-MTAB-6592:Sample 7

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-6592:Sample 7

characteristic: Submitter Id

text: ArrayExpress

text: human

text: late embryo

text: normal

text: Homo sapiens

text: Homo sapiens

text: urinary bladder

text: Homo sapiens

text: Sample 7


E-MTAB-6592:Sample 8

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-6592:Sample 8

text: ArrayExpress

characteristic: broker name

text: human

text: late embryo

text: normal

text: Homo sapiens

text: Homo sapiens

text: urinary bladder

text: Homo sapiens

text: Sample 8


E-MTAB-6592:Sample 9

characteristic: INSDC center name

text: public

text: E-MTAB-6592:Sample 9

characteristic: age

text: ArrayExpress

text: human

text: late embryo

text: normal

text: Homo sapiens

text: Homo sapiens

text: urinary bladder

text: Homo sapiens

text: Sample 9

characteristic: title


text: 445 N Fifth St

text: public

tag: Namespace:445 N Fifth St

characteristic: collection date

text: human

characteristic: common name

text: Temperate Forest

characteristic: environment (biome)

text: city

characteristic: environment (feature)

text: human

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Homo sapiens

characteristic: project name

text: Homo sapiens

text: Illumina

characteristic: sequencing method

text: GBM12 sequencing samples


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BIHP, INSTITUT PASTEUR

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:BIHP, INSTITUT PASTEUR

characteristic: Submitter Id

text: Human erythrocytes

characteristic: cell type

text: Asexual stages

characteristic: dev stage

text: Plasmodium falciparum 3D7

characteristic: organism

text: Plasmodium falciparum 3D7

text: hmeDIP-seq of Plasmodium falciparum asexual stages


text: BIHP, INSTITUT PASTEUR

characteristic: INSDC center name

text: public

text: Human erythrocytes

text: Asexual stages

text: Plasmodium falciparum 3D7

text: Plasmodium falciparum 3D7

text: RNA-seq of WGBS/WGoBS samples of Plasmodium falciparum

characteristic: title


text: BIHP, INSTITUT PASTEUR

text: public

text: Human erythrocytes

text: Asexual stages

text: Plasmodium falciparum 3D7

text: Plasmodium falciparum 3D7

text: BS-/oxBS-seq of Plasmodium falciparum asexual stages


text: public

tag: Namespace:DST/NRF Centre of Excellence for Biomedical TB research, SAMRC Centre for TB Research

characteristic: collection date

text: France

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: Various

characteristic: isolate

text: Human

characteristic: isolation source

text: Mycobacterium africanum

text: Mycobacterium africanum

text: MAF


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DST/NRF Centre of Excellence for Biomedical TB research, SAMRC Centre for TB Research

text: public

text: France

text: diseased

text: Homo sapiens

text: Various

text: Human

text: Mycobacterium africanum

text: Mycobacterium africanum

text: MAF


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: France

text: diseased

text: Homo sapiens

text: various

text: Human

text: Mycobacterium africanum

text: Mycobacterium africanum

text: MAF


text: THE OHIO STATE UNIVERSITY

text: public

tag: Namespace:THE OHIO STATE UNIVERSITY

characteristic: Submitter Id

text: uncultured bacterium

characteristic: organism

text: uncultured bacterium

text: 16s gene


text: THE OHIO STATE UNIVERSITY

characteristic: INSDC center name

text: public

text: uncultured bacterium

text: uncultured bacterium

characteristic: title


text: CNGB

text: public

text: Shizhong Li

characteristic: biomaterial provider

text: CNSA

characteristic: broker name

text: Xiaofen Fu

characteristic: collected by

characteristic: collection date

text: baker's yeast

characteristic: common name

text: China: Beijing

characteristic: geo loc name

text: Fermentation mixture of crushed sweet sorghum stalks

text: Saccharomyces cerevisiae

text: Pure culture

characteristic: sample type

text: Saccharomyces cerevisiae

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

tag: Namespace:Chengdu research base of giant panda breeding

text: giant panda

characteristic: environment (biome)

text: gut

characteristic: environment (feature)

text: fecal

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: metagenome

text: Study for giant panda gut microbiota and cellulose digestion mechanism

characteristic: project name

text: metagenome

text: Hiseq Illumina

characteristic: sequencing method


text: iiii

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: gut microbiota

characteristic: description

text: gut

text: gut

text: stool

text: Italy

text: human-gut

characteristic: human gut environmental package

text: metagenome

text: metagenomes

characteristic: organism

text: sardinian gut microbiota

text: metagenomes

text: pyrosequencing

text: sardinian gut microbiota

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: iiii

text: public

text: gut

characteristic: environment (biome)

text: gut

characteristic: environment (feature)

text: stool

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: human-gut

text: metagenome

text: metagenomes

text: sardinian gut microbiota

text: metagenomes

text: pyrosequencing

text: sardinian gut microbiota


text: SMU

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: feces metagenome

characteristic: common name

text: feces metagenome

text: feces metagenome

text: Male


text: SMU

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: feces metagenome

text: feces metagenome

text: feces metagenome

text: Female


text: public

tag: Namespace:NATIONAL INSTITUTE FOR HEALTH AND WELFARE

text: TB WGS

characteristic: description

text: Mycobacterium tuberculosis

characteristic: organism

text: Mycobacterium tuberculosis

text: TB WGS

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: CHUV-UNIL

text: public

characteristic: collection date

text: Complete genome sequence of Corynebacterium diphtheriae subp. lausannense strain CHUV2995. Isolated from a patient with severe tracheo-bronchitis.

text: Switzerland

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Broncho-alveolar lavage

characteristic: isolation source

text: Corynebacterium diphtheriae

text: Corynebacterium diphtheriae

characteristic: strain


characteristic: External Id

text: EMBL Heidelberg

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:EMBL Heidelberg

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: mouse embryonic stem cell

characteristic: cell type

text: house mouse

text: Protocols: Sox1-GFP mouse embryonic stem cells derived from the E14tg2a line (46C, (Ying et al., 2003)) were used. Sox1-GFP mouse embryonic stem cells derived from the E14tg2a line (46C, (Ying et al., 2003)) were grown at 37 °C in a 5% (v/v) CO2 incubator in GMEM (Invitrogen) supplemented with 10% (v/v) fetal bovine serum (FBS, Sigma), 2 ng/ml leukemia inhibitory factor (LIF, in-house), 1 mM 2-mercaptoethanol, non-essential amino acids (Gibco), L-glutamine (Gibco) and Na-pyruvate (Gibco), on gelatin-coated (0.1% v/v) plates. Accutase (Sigma) was used for cell dissociation. Cells were passaged every second day and seeded at a density of 1.3 million cells per 10 cm in surface area of the corresponding culture vessel. Medium was exchanged daily Libraries were produced following the in-situ HiC protocol published in Rao et al., 2014. In brief, cells were grown till 85% confluency and detached using Accutase. Cells were washed once in culture medium and once in PBS. 25M cell pellet was re-suspended in 50 ml medium and formaldehyde was added to a final concentration of 1%. Cells were incubated at room temperature with occasional mixing. The, 2.5ml of 2.5M Glycine was added and the reaction incubated for additional 5 minutes at room temperature. Cells were washed 2 times with ice cold PBS. Pellets were stored at -80. On the day of the experiment, 5M cell pellet were thawed for 10 minutes on ice. Cells were resuspended in 200 µl of lysis buffer (10mM Tris-HCl pH8.0, 10mM NaCl, 0.2% Igepal CA630)) supplemented with 50µl of protease inhibitors (Sigma, P8340) for 15 minutes on ice. Nuclei were spun and washed once in lysis buffer. Nuclei were resuspended in 50 µl of 0.5% SDS and incubated at 62°C for 5 minutes. Sammples were next chilled to room temperature, 145μl of water and 25μl of 10% Triton X-100 was added and nuclei were incubated for 15 minutes at 37°C. Next, 25μl of 10X NEBuffer2 and 100U of MboI restriction enzyme (NEB, R0147) was added and chromatin digested overnight at 37°C with rotation. MboI was inactivated at 62°C for 20 minutes. DNA ends were labelled with biotinylated dATP. To this end 30 µl of the following mix was added to the sample: 37.5μl of 0.4mM biotin-14-dATP (Life Technologies, 19524-016), 1.5μl of 10mM dCTP, 1.5μl of 10mM dGTP, 1.5μl of 10mM dTTP and 8μl of 5U/μl DNA Polymerase I, Large (Klenow) Fragment (NEB, M0210). Samples were incubated for 1.5 hours at 37°C with rotation. Then 900µl of ligation mix was added: 663μl of water, 120μl of 10X NEB T4 DNA ligase buffer (NEB, B0202), 100μl of 10% Triton X-100, 12μl of 10mg/ml Bovine Serum Albumin, 5μl of 400 U/ μl T4 DNA Ligase (NEB, M0202). Sampleswere incubated at room temperature for 4 hours with rotation. 50µl of 20mg/ml proteinase K 1and 20μl of 10% SDS were next added and the sample incubated for at 55°C for 30 minutes. Next, 130μl of 5M sodium chloride was added and the sample incubated at 68°C overnight. DNA was precipitated with 2 volumes of ethanol and washed 2 times with 75% ethanol. Pellet was air-dried and re-suspended in 100 µl of TE (10mM Tris, pH=8, 1mM EDTA). DNA was sheared to an average size of 400 bp using Covaris S2 apparatus. To size select fragments between 300 and 500 bp, 200 µl of DNA solution was mixed with 110μl (0.55X volumes) of AMPure XP beads (Beckman Coulter, A63881). Mix was incubated at room temperature for 5 minutes. Beads were separated on a magnet. The clear solution transferred to a fresh tube, 30μl of AMPure XP beads were added to the solution and incubated at room temperature for 5 minutes. Supernatant was discarded and the beads washed twice with 70% ethanol. DNA was eluted with 150 µl of 10 mM tris, pH=8. Biotinylated DNA was pulled down using streptavidin T1 beads (150 µl per reaction, washed once in Tween Wash Buffer: (1X TWB: 5mM Tris-HCl (pH 7.5); 0.5mM EDTA; 1M NaCl; 0.05% Tween 20) and re-suspended in 150µl of 2x Binding buffer (2X BB: 10mM Tris-HCl (pH 7.5); 1mM EDTA; 2M NaCl). Sample was incubated for 30 minutes at room temperature with mixing. After the incubation, beads were washed twice by incubating at 55°C for 2 min with 600 µl of 1xTWB (at each wash, the beads were separated from the wash buffer on magnet and the buffer discarded). Beads were washed once in 1x DNA ligase buffer. After this wash, beads were incubated at room temperature for 30 minutes with the blunting mix: 88μl of 1X NEB T4 DNA ligase buffer with 10mM ATP, 2μl of 25mM dNTP mix, 5μl of 10U/μl NEB T4 PNK (NEB, M0201), 4μl of 3U/μl NEB T4 DNA polymerase I (NEB, M0203), 1μl of 5U/μl NEB DNA polymerase I, Large (Klenow) Fragment (NEB, M0210). Beads were washed twice in TWB as indicated above and once in 100 µl 1x NEB buffer 2. Next neads were incubated at 37°C for 30 minutes with 100μl of dATP attachment master mix (90μl of 1X NEBuffer 2, 5μl of 10mM dATP, 5μl of 5U/μl NEB Klenow exo minus (NEB, M0212)). Beads were washed twice with 1x TWB (as above) and once with 100 µl of 1x quick ligation buffer (NEB M2200). Beads were re-suspended in 50 µl of quick ligation buffer and mixed with 3μl of an Illumina indexed adapter and 2 µl of quick ligase. After a 15 minute incubation, beads were washed twice with 1x TWB as above. Beads were re-suspended in 50 µl of 10 mM This, pH=8. Five amplification reactions were set, in each 5 µl of beads were mixed with 4 µl of 12.5 µM illumina primers and 25 µl of 2xphusion master mix and 16 µl of water. Samples were amplified for 6 cycles (according to manufacturer’s recommendations). DNA was purified using AmpureXP beads (60µl per 50 µl PCR reaction).

characteristic: genotype

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: mouse embryonic stem cell

characteristic: progenitor cell type

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMBL Heidelberg

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: neuronal stem cell

text: house mouse

characteristic: common name

text: Protocols: Sox1-GFP mouse embryonic stem cells derived from the E14tg2a line (46C, (Ying et al., 2003)) were used. ES cells were plated at a density of 0.8 million cells per gelatin-coated 10 cm culture vessels in 50% DMEM, 50% F12 (DMEM/F12, Invitrogen) medium supplemented with 2.5ml of N2 and 5ml of B27 (Gibco), BSA (Gibco, final concentration of 0.012%), non-essential amino acids (Gibco), glucose (final concentration 0.03 M), HEPES (final concentration 4.5 mM) and 0.1 mM beta-mercaptoethanol (differentiation medium). Medium was exchanged after 24 and 48 hours, and the cultures were grown for an additional 72 hours. Cells were then gently dissociated using Accutase (Sigma), the GFP+ cell fraction (corresponding to ca. 70% of cells) was sorted by flow cytometry and seeded into a laminin (Sigma) coated 75 cm2 flask (final density of laminin: 10 µg/cm2 of culture surface, coating time: minimum 4 hours at 37°C). Subsequently, cells were grown in differentiation medium supplemented with in-house prepared recombinant murine EGF and bFGF (final concentration of 10 ng/ml) until loss of GFP expression and uniform upregulation of Nestin expression was observed by immunostaining and qRT-PCR. NS cells were passaged at 80% confluence. Medium was exchanged daily. Libraries were produced following the in-situ HiC protocol published in Rao et al., 2014. In brief, cells were grown till 85% confluency and detached using Accutase. Cells were washed once in culture medium and once in PBS. 25M cell pellet was re-suspended in 50 ml medium and formaldehyde was added to a final concentration of 1%. Cells were incubated at room temperature with occasional mixing. The, 2.5ml of 2.5M Glycine was added and the reaction incubated for additional 5 minutes at room temperature. Cells were washed 2 times with ice cold PBS. Pellets were stored at -80. On the day of the experiment, 5M cell pellet were thawed for 10 minutes on ice. Cells were resuspended in 200 µl of lysis buffer (10mM Tris-HCl pH8.0, 10mM NaCl, 0.2% Igepal CA630)) supplemented with 50µl of protease inhibitors (Sigma, P8340) for 15 minutes on ice. Nuclei were spun and washed once in lysis buffer. Nuclei were resuspended in 50 µl of 0.5% SDS and incubated at 62°C for 5 minutes. Sammples were next chilled to room temperature, 145μl of water and 25μl of 10% Triton X-100 was added and nuclei were incubated for 15 minutes at 37°C. Next, 25μl of 10X NEBuffer2 and 100U of MboI restriction enzyme (NEB, R0147) was added and chromatin digested overnight at 37°C with rotation. MboI was inactivated at 62°C for 20 minutes. DNA ends were labelled with biotinylated dATP. To this end 30 µl of the following mix was added to the sample: 37.5μl of 0.4mM biotin-14-dATP (Life Technologies, 19524-016), 1.5μl of 10mM dCTP, 1.5μl of 10mM dGTP, 1.5μl of 10mM dTTP and 8μl of 5U/μl DNA Polymerase I, Large (Klenow) Fragment (NEB, M0210). Samples were incubated for 1.5 hours at 37°C with rotation. Then 900µl of ligation mix was added: 663μl of water, 120μl of 10X NEB T4 DNA ligase buffer (NEB, B0202), 100μl of 10% Triton X-100, 12μl of 10mg/ml Bovine Serum Albumin, 5μl of 400 U/ μl T4 DNA Ligase (NEB, M0202). Sampleswere incubated at room temperature for 4 hours with rotation. 50µl of 20mg/ml proteinase K 1and 20μl of 10% SDS were next added and the sample incubated for at 55°C for 30 minutes. Next, 130μl of 5M sodium chloride was added and the sample incubated at 68°C overnight. DNA was precipitated with 2 volumes of ethanol and washed 2 times with 75% ethanol. Pellet was air-dried and re-suspended in 100 µl of TE (10mM Tris, pH=8, 1mM EDTA). DNA was sheared to an average size of 400 bp using Covaris S2 apparatus. To size select fragments between 300 and 500 bp, 200 µl of DNA solution was mixed with 110μl (0.55X volumes) of AMPure XP beads (Beckman Coulter, A63881). Mix was incubated at room temperature for 5 minutes. Beads were separated on a magnet. The clear solution transferred to a fresh tube, 30μl of AMPure XP beads were added to the solution and incubated at room temperature for 5 minutes. Supernatant was discarded and the beads washed twice with 70% ethanol. DNA was eluted with 150 µl of 10 mM tris, pH=8. Biotinylated DNA was pulled down using streptavidin T1 beads (150 µl per reaction, washed once in Tween Wash Buffer: (1X TWB: 5mM Tris-HCl (pH 7.5); 0.5mM EDTA; 1M NaCl; 0.05% Tween 20) and re-suspended in 150µl of 2x Binding buffer (2X BB: 10mM Tris-HCl (pH 7.5); 1mM EDTA; 2M NaCl). Sample was incubated for 30 minutes at room temperature with mixing. After the incubation, beads were washed twice by incubating at 55°C for 2 min with 600 µl of 1xTWB (at each wash, the beads were separated from the wash buffer on magnet and the buffer discarded). Beads were washed once in 1x DNA ligase buffer. After this wash, beads were incubated at room temperature for 30 minutes with the blunting mix: 88μl of 1X NEB T4 DNA ligase buffer with 10mM ATP, 2μl of 25mM dNTP mix, 5μl of 10U/μl NEB T4 PNK (NEB, M0201), 4μl of 3U/μl NEB T4 DNA polymerase I (NEB, M0203), 1μl of 5U/μl NEB DNA polymerase I, Large (Klenow) Fragment (NEB, M0210). Beads were washed twice in TWB as indicated above and once in 100 µl 1x NEB buffer 2. Next neads were incubated at 37°C for 30 minutes with 100μl of dATP attachment master mix (90μl of 1X NEBuffer 2, 5μl of 10mM dATP, 5μl of 5U/μl NEB Klenow exo minus (NEB, M0212)). Beads were washed twice with 1x TWB (as above) and once with 100 µl of 1x quick ligation buffer (NEB M2200). Beads were re-suspended in 50 µl of quick ligation buffer and mixed with 3μl of an Illumina indexed adapter and 2 µl of quick ligase. After a 15 minute incubation, beads were washed twice with 1x TWB as above. Beads were re-suspended in 50 µl of 10 mM This, pH=8. Five amplification reactions were set, in each 5 µl of beads were mixed with 4 µl of 12.5 µM illumina primers and 25 µl of 2xphusion master mix and 16 µl of water. Samples were amplified for 6 cycles (according to manufacturer’s recommendations). DNA was purified using AmpureXP beads (60µl per 50 µl PCR reaction).

characteristic: description

text: Mus musculus

characteristic: organism

text: Mus musculus

text: mouse embryonic stem cell

text: Mus musculus

characteristic: title


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, 69120 Heidelberg, Germany DZHK (German Centre for Cardiovascular Research), Partner site Heidelberg/Mannheim, 69120 Heidelberg, Germany

text: ArrayExpress

text: HeLa

text: epithelial cell

text: human

text: Protocols: HeLa Flp-In T-REx cells were cultured in DMEM supplemented with 9% fetal bovine serum and 1x Penicillin Streptomycin. The cells were cultivated at 37°C and 5% CO2 in a humidified incubator. For siRNA transfection, cells were reverse transfected with 60 pmol siRNA targeting RNPS1 (or Luc in the negative control) per 2 x 10^5 cells using 2.5 μl Lipofectamine RNAiMAX. For rescue, for generating stable RNPS1 rescue cell lines, the expression constructs were cloned into the pcDNA5/FRT/TO vector containing an N-terminal FLAG-tag. Standard protocols were used to generate stable rescue or reporter HeLa Flp-In T-REx cell lines and positive clones were selected with 100-150 μg/ml hygromycin B. Expression of stable cell lines was induced with 1 μg/ml doxycycline 24 h after siRNA transfection. Fresh medium with 1 μg/ml doxycycline was added after additional 48 h. The H176D-E179R mutation of a surface exposed patch of RNPS1 prevents ASAP complex formation. Total RNA was extracted with peqGOLD TriFast according to the manufacturer's instructions. Ribosomal depletion and strand specific library preparation was carried out with the TruSeq R Stranded Total RNA LT (with Ribo-ZeroTM Human/Mouse/Rat) according to the manufacturer's instructions.

text: cervical adenocarcinoma

characteristic: disease

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: uterine cervix

characteristic: organism part

text: wild type phenotype

characteristic: phenotype

text: Luc knockdown by siRNA

characteristic: rna interference

text: Homo sapiens


tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, 69120 Heidelberg, Germany DZHK (German Centre for Cardiovascular Research), Partner site Heidelberg/Mannheim, 69120 Heidelberg, Germany

text: public

text: ArrayExpress

characteristic: broker name

text: HeLa

characteristic: cell line

text: epithelial cell

characteristic: cell type

text: human

text: cervical adenocarcinoma

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: uterine cervix

text: wild type phenotype

text: Luc knockdown by siRNA

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: HeLa

text: epithelial cell

text: human

characteristic: common name

characteristic: description

text: cervical adenocarcinoma

text: RNPS1 knockdown by siRNA

text: Homo sapiens

text: Homo sapiens

text: uterine cervix

text: RNPS1 knockdown

text: RNPS1 knockdown by siRNA

text: Homo sapiens


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: HeLa

text: epithelial cell

text: human

text: cervical adenocarcinoma

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: uterine cervix

text: RNPS1 knockdown and rescue with wild type RNPS1

text: RNPS1 knockdown by siRNA

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: HeLa

text: epithelial cell

text: human

text: cervical adenocarcinoma

characteristic: disease

text: pcDNA5/FRT/TO-RNPS1 H176D-E179R

text: Homo sapiens

text: Homo sapiens

text: uterine cervix

characteristic: organism part

text: RNPS1 knockdown and rescue with RNPS1 loss of function mutant

characteristic: phenotype

text: RNPS1 knockdown by siRNA

characteristic: rna interference

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

tag: Namespace:MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY

characteristic: collection date

text: Marine sediment ciliate Kentrophoros sp. H and associated bacteria, sample SA2B15. Single ciliate cell fixed for DNA/RNA sequencing. Corresponds to JGI GOLD Biosample ID Gb0112758.

text: marine neritic benthic zone biome

characteristic: environment (biome)

text: sea grass bed

characteristic: environment (feature)

text: shallow marine sediment

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Isola d'Elba; Sant' Andrea

characteristic: geographic location (region and locality)

text: Kentrophoros sp. H

characteristic: host common name

characteristic: host taxid

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: ciliate metagenome

text: Metagenomics of Kentrophoros ciliate-bacteria symbiosis

characteristic: project name

text: decantation after stirring with seawater

characteristic: sample collection device or method

text: fixed in RNAlater

characteristic: sample material processing

text: ciliate metagenome

text: Illumina

characteristic: sequencing method

text: Kentrophoros sp. H sample SA2B15


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Marine sediment ciliate Kentrophoros sp. H and associated bacteria, sample SA2B20. Single ciliate cell fixed for DNA/RNA sequencing. Corresponds to JGI GOLD Biosample ID Gb0112765.

characteristic: description

text: marine neritic benthic zone biome

text: sea grass bed

text: shallow marine sediment

text: Italy

text: Isola d'Elba; Sant' Andrea

text: Kentrophoros sp. H

text: host-associated

text: metagenome

text: ciliate metagenome

characteristic: organism

text: fixed in RNAlater

text: ciliate metagenome

text: Illumina

text: Kentrophoros sp. H sample SA2B20

characteristic: title


text: public

text: Marine sediment ciliate Kentrophoros sp. H and associated bacteria, sample SA2B12. Single ciliate cell fixed for DNA/RNA sequencing. Corresponds to JGI GOLD Biosample ID Gb0112864.

text: marine neritic benthic zone biome

characteristic: environment (biome)

text: sea grass bed

characteristic: environment (feature)

text: shallow marine sediment

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Isola d'Elba; Sant' Andrea

characteristic: geographic location (region and locality)

text: Kentrophoros sp. H

characteristic: host common name

characteristic: host taxid

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: ciliate metagenome

characteristic: project name

characteristic: sample collection device or method

text: fixed in RNAlater

text: ciliate metagenome

text: Illumina

text: Kentrophoros sp. H sample SA2B12


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Marine sediment ciliate Kentrophoros sp. SD and associated bacteria, sample S127. Single ciliate cell fixed for DNA/RNA sequencing. Corresponds to JGI GOLD Biosample ID Gb0112865.

characteristic: description

text: marine neritic benthic zone biome

text: bay

text: shallow marine sediment

text: Italy

text: Isola d'Elba; Golfo di Barbatoia

text: Kentrophoros sp. SD

text: host-associated

text: metagenome

text: ciliate metagenome

text: Uhlig seawater ice method

text: fixed in RNAlater

characteristic: sample material processing

text: ciliate metagenome

text: Illumina

characteristic: sequencing method

text: Kentrophoros sp. SD sample S127


text: public

text: Marine sediment ciliate Kentrophoros sp. SD and associated bacteria, sample S1320. Single ciliate cell fixed for DNA/RNA sequencing. Corresponds to JGI GOLD Biosample ID Gb0112866.

text: marine neritic benthic zone biome

characteristic: environment (biome)

text: bay

characteristic: environment (feature)

text: shallow marine sediment

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Isola d'Elba; Golfo di Barbatoia

characteristic: geographic location (region and locality)

text: Kentrophoros sp. SD

characteristic: host common name

characteristic: host taxid

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: ciliate metagenome

characteristic: organism

text: Uhlig seawater ice method

text: fixed in RNAlater

text: ciliate metagenome

text: Illumina

text: Kentrophoros sp. SD sample S1320

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Marine sediment ciliate Kentrophoros sp. SD and associated bacteria, sample S1321. Single ciliate cell fixed for DNA/RNA sequencing. Corresponds to JGI GOLD Biosample ID Gb0112867.

characteristic: description

text: marine neritic benthic zone biome

text: bay

text: shallow marine sediment

text: Italy

text: Isola d'Elba; Golfo di Barbatoia

text: Kentrophoros sp. SD

text: host-associated

text: metagenome

text: ciliate metagenome

characteristic: project name

text: Uhlig seawater ice method

characteristic: sample collection device or method

text: fixed in RNAlater

text: ciliate metagenome

text: Illumina

text: Kentrophoros sp. SD sample S1321


text: public

text: Marine sediment ciliate Kentrophoros sp. LPFa and associated bacteria, sample S312. Single ciliate cell fixed for DNA/RNA sequencing. Corresponds to JGI GOLD Biosample ID Gb0112868.

text: marine neritic benthic zone biome

characteristic: environment (biome)

text: bay

characteristic: environment (feature)

text: shallow marine sediment

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Isola d'Elba; Golfo di Barbatoia

characteristic: geographic location (region and locality)

text: Kentrophoros sp. LPFa

characteristic: host common name

characteristic: host taxid

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: ciliate metagenome

text: Uhlig seawater ice method

text: fixed in RNAlater

characteristic: sample material processing

text: ciliate metagenome

text: Illumina

characteristic: sequencing method

text: Kentrophoros sp. LPFa sample S312


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Marine sediment ciliate Kentrophoros sp. LPFa and associated bacteria, sample S313. Single ciliate cell fixed for DNA/RNA sequencing. Corresponds to JGI GOLD Biosample ID Gb0112869.

characteristic: description

text: marine neritic benthic zone biome

text: bay

text: shallow marine sediment

text: Italy

text: Isola d'Elba; Golfo di Barbatoia

text: Kentrophoros sp. LPFa

text: host-associated

text: metagenome

text: ciliate metagenome

characteristic: organism

text: Uhlig seawater ice method

text: fixed in RNAlater

text: ciliate metagenome

text: Illumina

text: Kentrophoros sp. LPFa sample S313

characteristic: title


text: public

text: Marine sediment ciliate Kentrophoros sp. LPFa and associated bacteria, sample S426. Single ciliate cell fixed for DNA/RNA sequencing. Corresponds to JGI GOLD Biosample ID Gb0112870.

text: marine neritic benthic zone biome

characteristic: environment (biome)

text: bay

characteristic: environment (feature)

text: shallow marine sediment

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Isola d'Elba; Golfo di Barbatoia

characteristic: geographic location (region and locality)

text: Kentrophoros sp. LPFa

characteristic: host common name

characteristic: host taxid

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: ciliate metagenome

characteristic: project name

text: Uhlig seawater ice method

characteristic: sample collection device or method

text: fixed in RNAlater

text: ciliate metagenome

text: Illumina

text: Kentrophoros sp. LPFa sample S426


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Marine sediment ciliate Kentrophoros sp. LFY and associated bacteria, sample M6. Single ciliate cell fixed for DNA/RNA sequencing. Corresponds to JGI GOLD Biosample ID Gb0112871.

characteristic: description

text: marine neritic benthic zone biome

text: sea grass bed

text: shallow marine sediment

text: Italy

text: Isola d'Elba; Cavoli

text: Kentrophoros sp. LFY

text: host-associated

text: metagenome

text: ciliate metagenome

text: fixed in RNAlater

characteristic: sample material processing

text: ciliate metagenome

text: Illumina

characteristic: sequencing method

text: Kentrophoros sp. LFY sample M6


text: public

text: Marine sediment ciliate Kentrophoros sp. LFY and associated bacteria, sample M7. Single ciliate cell fixed for DNA/RNA sequencing. Corresponds to JGI GOLD Biosample ID Gb0112872.

text: marine neritic benthic zone biome

characteristic: environment (biome)

text: sea grass bed

characteristic: environment (feature)

text: shallow marine sediment

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Isola d'Elba; Cavoli

characteristic: geographic location (region and locality)

text: Kentrophoros sp. LFY

characteristic: host common name

characteristic: host taxid

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: ciliate metagenome

characteristic: organism

text: fixed in RNAlater

text: ciliate metagenome

text: Illumina

text: Kentrophoros sp. LFY sample M7

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Marine sediment ciliate Kentrophoros sp. LFY and associated bacteria, sample BY7. Single ciliate cell fixed for DNA/RNA sequencing. Corresponds to JGI GOLD Biosample ID Gb0112873.

characteristic: description

text: marine neritic benthic zone biome

text: sea grass bed

text: shallow marine sediment

text: Italy

text: Isola d'Elba; Cavoli

text: Kentrophoros sp. LFY

text: host-associated

text: metagenome

text: ciliate metagenome

characteristic: project name

characteristic: sample collection device or method

text: fixed in RNAlater

text: ciliate metagenome

text: Illumina

text: Kentrophoros sp. LFY sample BY7


text: public

text: Marine sediment ciliate Kentrophoros sp. TUN and associated bacteria, sample BY1. Single ciliate cell fixed for DNA/RNA sequencing. Corresponds to JGI GOLD Biosample ID Gb0112874.

text: marine neritic benthic zone biome

characteristic: environment (biome)

text: sea grass bed

characteristic: environment (feature)

text: shallow marine sediment

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Isola d'Elba; Sant' Andrea

characteristic: geographic location (region and locality)

text: Kentrophoros sp. TUN

characteristic: host common name

characteristic: host taxid

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: ciliate metagenome

text: fixed in RNAlater

characteristic: sample material processing

text: ciliate metagenome

text: Illumina

characteristic: sequencing method

text: Kentrophoros sp. TUN sample BY1


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Marine sediment ciliate Kentrophoros sp. TUN and associated bacteria, sample BY2. Single ciliate cell fixed for DNA/RNA sequencing. Corresponds to JGI GOLD Biosample ID Gb0112875.

characteristic: description

text: marine neritic benthic zone biome

text: sea grass bed

text: shallow marine sediment

text: Italy

text: Isola d'Elba; Sant' Andrea

text: Kentrophoros sp. TUN

text: host-associated

text: metagenome

text: ciliate metagenome

characteristic: organism

text: fixed in RNAlater

text: ciliate metagenome

text: Illumina

text: Kentrophoros sp. TUN sample BY2

characteristic: title


text: public

text: Marine sediment ciliate Kentrophoros sp. TUN and associated bacteria, sample BY3. Single ciliate cell fixed for DNA/RNA sequencing. Corresponds to JGI GOLD Biosample ID Gb0112876.

text: marine neritic benthic zone biome

characteristic: environment (biome)

text: sea grass bed

characteristic: environment (feature)

text: shallow marine sediment

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Isola d'Elba; Sant' Andrea

characteristic: geographic location (region and locality)

text: Kentrophoros sp. TUN

characteristic: host common name

characteristic: host taxid

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: ciliate metagenome

characteristic: project name

characteristic: sample collection device or method

text: fixed in RNAlater

text: ciliate metagenome

text: Illumina

text: Kentrophoros sp. TUN sample BY3


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Marine sediment ciliate Kentrophoros sp. UNK and associated bacteria, sample BY8. Single ciliate cell fixed for DNA/RNA sequencing. Corresponds to JGI GOLD Biosample ID Gb0112877.

characteristic: description

text: marine neritic benthic zone biome

text: sea grass bed

text: shallow marine sediment

text: Italy

text: Isola d'Elba; Cavoli

text: Kentrophoros sp. UNK

text: host-associated

text: metagenome

text: ciliate metagenome

text: Metagenomics of Kentrophoros ciliate-bacteria symbiosis

text: fixed in RNAlater

characteristic: sample material processing

text: ciliate metagenome

text: Illumina

characteristic: sequencing method

text: Kentrophoros sp. UNK sample BY8


text: MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY

text: public

text: Marine sediment ciliate Kentrophoros sp. UNK and associated bacteria, sample BY19. Single ciliate cell fixed for DNA/RNA sequencing. Corresponds to JGI GOLD Biosample ID Gb0112878.

text: marine neritic benthic zone biome

characteristic: environment (biome)

text: sea grass bed

characteristic: environment (feature)

text: shallow marine sediment

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Isola d'Elba; Cavoli

characteristic: geographic location (region and locality)

text: Kentrophoros sp. UNK

characteristic: host common name

characteristic: host taxid

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: ciliate metagenome

characteristic: organism

text: decantation after stirring with seawater

text: fixed in RNAlater

text: ciliate metagenome

text: Illumina

text: Kentrophoros sp. UNK sample BY19

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Marine sediment ciliate Kentrophoros sp. FM and associated bacteria, sample BZ163. Single ciliate cell fixed for DNA/RNA sequencing. Corresponds to JGI GOLD Biosample ID Gb0132593.

characteristic: description

text: marine neritic benthic zone biome

text: mangrove island

text: shallow marine sediment

text: Belize

text: Twin Cayes; Fisheries Beach

text: Kentrophoros sp. FM

text: host-associated

text: metagenome

text: ciliate metagenome

characteristic: project name

text: Uhlig seawater ice method

characteristic: sample collection device or method

text: fixed in RNAlater

text: ciliate metagenome

text: Illumina

text: Kentrophoros sp. FM sample BZ163