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RNASeq Ascaris suum

Ascaris suum - public RNASeq studies

Analysed

SRP005511: Ascaris suum transcriptome (RNA-Seq) data

Richard E. Davis Lab, Biochemistry and Molecular Genetics, University of Colorado Denver

Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles. (Wang .. Davis, 2011)

Design: 6 conditions

Condition num. replicates Developmental stage Organism part Sex
L2 larvae 1 L2 whole organism mixed
embryos 5 embryo 0 - 64 hr whole organism mixed
female reproductive system 1 adult female reproductive system female
ovary 1 adult ovary female
testis 6 adult testis male
whole male 1 adult whole organism male

SRP010159: Ascaris suum Genome sequencing

Beijing Genomics Institute

Ascaris suum draft genome. (Jex .. Gasser, 2011)

Design: 8 conditions

Condition num. replicates Developmental stage Geographic location Host Host tissue Individual Sex
Adult female individual 1 1 adult Belgium Sus scrofa 1 female
Adult female individual 2 1 adult Belgium Sus scrofa 2 female
Adult male individual 3 1 adult Belgium Sus scrofa 3 male
Adult male individual 4 1 adult Belgium Sus scrofa 4 male
Pooled L3 stage eggs 1 egg Belgium Sus scrofa mixed
Pooled L3 stage from pig lungs 1 L3 Belgium Sus scrofa lungs mixed
Pooled L3 stage isolated from pig livers 1 L3 Belgium Sus scrofa liver mixed
Pooled L4 stage from pig small intestine 1 L4 Belgium Sus scrofa small intestine mixed

SRP013573: Silencing of Germline-Expressed Genes by DNA Elimination in Somatic Cells

Richard E. Davis Lab, Biochemistry and Molecular Genetics, University of Colorado Denver

Silencing of germline-expressed genes by DNA elimination in somatic cells. (Wang .. Davis, 2012)

Design: 10 conditions

Condition num. replicates Developmental stage Organism part Sample name Source name Strain Timepoint
24hr 1 embryo 24hr 24hr (1-cell) embryos North American wild population 24 hr
46hr 1 embryo 46hr 46hr (1-2-cell) embryos North American wild population 46 hr
64hr 1 embryo 64hr 64hr (2-4-cell) embryos North American wild population 64 hr
female carcass 1 adult carcass female carcass muscle, hypodermis, pharynx, and neurons North American wild population
intestine 1 adult intestine intestine intestine North American wild population
larvae 1 larvae larvae 7 days - Larvae L2 North American wild population
male carcass 1 adult carcass male carcass muscle, hypodermis, pharynx, and neurons North American wild population
muscle 1 adult muscle muscle muscle (and hypodermis) North American wild population
ovary 1 adult ovary ovary ovary germinal zone North American wild population
testis 1 adult testis testis testis germinal zone North American wild population

SRP021466: Transcription in Pronuclei and One- to Four-Cell Embryos Drives Early Development in a Nematode

Richard E. Davis Lab, Biochemistry and Molecular Genetics, University of Colorado Denver

Transcription in pronuclei and one- to four-cell embryos drives early development in a nematode. (Wang .. Davis, 2014)

Design: 16 conditions

Condition num. replicates Developmental stage Sample name Source name Strain Timepoint
embryo, 1 day 1 embryo North American wild population 1 day
embryo, 116 hours 1 embryo North American wild population 116 hours
embryo, 2h hours 1 embryo North American wild population 2h hours
embryo, 3 days 1 embryo North American wild population 3 days
embryo, 46 hours 1 embryo North American wild population 46 hours
embryo, 5 days 1 embryo North American wild population 5 days
embryo, 64 hours 3 embryo North American wild population 64 hours
embryo, 7 days 2 embryo North American wild population 7 days
embryo, 96 hours 1 embryo North American wild population 96 hours
larvae, L1 1 larvae North American wild population L1
oocyte - ribozero 1 female germline oocyte - ribozero oocyte North American wild population
oocyte - total 1 female germline oocyte - total oocyte North American wild population
oocyte with wall 1 female germline oocyte with wall oocyte with wall North American wild population
oocyte with wall - ribozero 1 female germline oocyte with wall - ribozero oocyte with wall North American wild population
oocyte with wall - total 1 female germline oocyte with wall - total oocyte with wall North American wild population
zygote 7 zygote North American wild population

SRP108384: Comparative Genome Analysis of Programmed DNA Elimination in Nematodes (Ascaris)

Richard E. Davis Lab, Biochemistry and Molecular Genetics, University of Colorado Denver

Comparative genome analysis of programmed DNA elimination in nematodes. (Wang .. Davis, 2017)

Design: 10 conditions

Condition num. replicates Organism part Sex Strain
Female diplotene 1 diplotene Female North American wildtype
Female early pachytene 1 early pachytene Female North American wildtype
Female late pacheytene 1 late pacheytene Female North American wildtype
Female mitotic region 1 mitotic region Female North American wildtype
Female oocyte 1 oocyte Female North American wildtype
Male mitotic region 1 mitotic region Male North American wildtype
Male post-meiotic region 1 post-meiotic region Male North American wildtype
Male seminal vesicle 1 seminal vesicle Male North American wildtype
Male spermatids 1 spermatids Male North American wildtype
Male spermatogenesis 1 spermatogenesis Male North American wildtype

SRP140708: Dual RNA-Seq of Ascaris suum larvae (L3) and Sus scrofa cells (IPEC-J2)

Robert Koch Insitute

Design: 5 conditions

Condition num. replicates Developmental stage Host tissue Timepoint
0 hours 3 L3 stage larvae porcine intestinal epithelial cells (IPEC-J2) 0 hours
1 hours 2 L3 stage larvae porcine intestinal epithelial cells (IPEC-J2) 1 hours
2 hours 3 L3 stage larvae porcine intestinal epithelial cells (IPEC-J2) 2 hours
3 hours 3 L3 stage larvae porcine intestinal epithelial cells (IPEC-J2) 3 hours
9 hours 3 L3 stage larvae porcine intestinal epithelial cells (IPEC-J2) 9 hours

Other

These studies are available in ENA, and the reads successfully align to our genomes.
We have decided not to include them in our analysis.
Either they failed to meet minimal criteria for inclusion, we've been asked to exclude them for data quality reasons, or we were unable to interpret the metadata.

SRP005510: Ascaris suum Small RNA-Seq data

Richard E. Davis Lab, Biochemistry and Molecular Genetics, University of Colorado Denver

Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles. (Wang .. Davis, 2011)

1 runs in ENA

SRP013430: Ascaris suum Chromatin Diminution

University of Colorado School of Medicine

10 runs in ENA

SRP013609: De novo nematode genome sequencing project to sequence, Ascaris suum, or Pig Roundworm.

The Genome Institute

87 runs in ENA