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accession-icon SRP044629
Mus musculus strain:a C57BL/6;129/SvEv mixed background Transcriptome or Gene expression
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer II

Description

To investigate the molecular mechanism which caused the defect of aberrant somatic cell differentiation in Wt1-deficient gonads, the differentially expressed genes between control and Wt1-deficient gonads at E11.5 was analyzed by RNA Seq analysis.After tamoxifen injection at E9.5, total RNA was prepared from control and Wt1-deficient gonads at E11.5 using RNeasy Minikit (Ambion, Austin, TX). Gonads of the same genotype (about 12 pairs each) were pooled together. For RNA-Seq, the main reagents and instruments used for RNA library construction and deep sequencing were the Illumina Gene Expression Sample Prep Kit, Solexa Sequencing Chip (flowcell), Illumina Cluster Station and Illumina HiSeq 2000 System. Sequence tags were prepared using the Illumina Digital Gene Expression Tag Profiling Kit, according to the manufacturer's protocol. Raw data was filtered to remove adaptor tags, low quality tags, and tags with a single copy number. Paired-end reads were mapped to the mouse genome (mm9) with TopHat and further analyzed by Cufflinks-Cuffdiff (Trapnell et al., 2009; Trapnell et al., 2010) pipelines to identify differentially expressed transcripts (DETs) between control and Wt1-deficient gonads.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP103621
Homo sapiens Transcriptome or Gene expression
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 4000

Description

Ovaries differentiated by hair follicle stem cells, and normal eggs in the body, for transcriptome analysis

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Specimen part

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accession-icon SRP069329
Homo sapiens male germ cell transcriptome
  • organism-icon Homo sapiens
  • sample-icon 34 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2000

Description

Goal of this study is to identify the transcriptome of human male germ cell subtypes during normal spermatogenesis as a reference for subfertility.

Publication Title

Unraveling transcriptome dynamics in human spermatogenesis.

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP099280
Human meiotic arrest
  • organism-icon Homo sapiens
  • sample-icon 15 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Molecular mechanism of human meiotic arrest

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Specimen part

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accession-icon E-MEXP-1211
Transcription profiling of uteri from mice in which the uterine lumen were transiently-transfected with a plasmid harboring HOXA10
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

nulliparous cd1 female mice were mated. Twenty four hours after detecting hte vaginal plug , the animals were laparatomized and the uterine lumen were transiently-transfected with plasmid harboring HOXA10 or control. Forty eight hours later, the uteri were morcellated in trizol and the RNA was extracted per Trizol protocol. Total RNA was then submitted for microarray analysis

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Age, Specimen part, Subject

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accession-icon GSE23009
Effect of intra-cytoplasmic sperm injection (ICSI) on gene expression and development of mouse preimplantation embryos
  • organism-icon Mus musculus
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Background: In vitro culture of preimplantation mouse embryos is associated with changes in gene expression. It is however not known if the method of fertilization affects the global pattern of gene expression. Method: We compared gene expression and development of mouse blastocysts produced by intra-cytoplasmic sperm injection and cultured in Whittens medium (ICSIWM) or KSOM medium with amino acids (ICSIKSOMaa) with control blastocysts flushed out of the uterus on post coital day 3.5 (In vivo). Global pattern of gene expression was assessed using the Affymetrix 430 2.0 chip. In addition we compared gene expression in embryos generated in IVF or ICSI using WM. Results: Blastocysts resulting from ICSI fertilization have a reduction in the number of trophoblastic and inner cell mass cells compared to in vivo generated embryos. Approximately 1000 genes are different between ICSI blastocyst and in vivo blastocysts; proliferation, apoptosis and morphogenetic pathways are the most common pathways altered after in vitro culture. Unexpectedly, only 41 genes were statistically different between embryo cultured in suboptimal conditions (WM) or optimal conditions (KSOMaa). Conclusion: The method of fertilization plays a more important role in shaping the transcriptome of the developing mouse embryo than the culture media used.

Publication Title

No associated publication

Alternate Accession IDs

E-GEOD-23009

Sample Metadata Fields

Specimen part

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accession-icon GSE29625
Human embryonic stem cells derived from embryos at different stages of development share similar transcription profiles
  • organism-icon Homo sapiens
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

We have derived hESC from biopsied blastomeres of cleavage stage embryos under virtually the same conditions we used for the derivation of hESC lines from inner cell mass of blastocyst stage embryos. Blastomere-derived hESC lines exhibited all the standard characteristics of hESC including undifferentiated proliferation, genomic stability, expression of pluripotency markers and the ability to differentiate into the cells of all three germ layers both in vitro and in vivo. To examine whether hESC lines derived from two developmental stages of the embryo differ in gene expression, we have subjected three blastomere-derived hESC lines and two ICM-derived hESC lines grown under identical culture conditions to transcriptome analysis using gene expression arrays. Unlike previously reported comparisons of hESC lines which demonstrated, apart from core hESC-associated pluripotency signature, significant variations in gene expression profiles of different lines, our data show that hESC lines derived and grown under well-controlled defined culture conditions adopt nearly identical gene expression profiles. Moreover, blastomere-derived and ICM-derived hESC exhibited very similar transcriptional profiles independent of the developmental stage of the embryo from which they originated. Furthermore, this profile was evident in very early passages of the cells and did not appear to be affected by extensive passaging. These results suggest that during derivation process cells which give rise to hESC acquire virtually identical stable phenotype and are not affected by the developmental stage of the starting cell population.

Publication Title

Human embryonic stem cells derived from embryos at different stages of development share similar transcription profiles.

Alternate Accession IDs

E-GEOD-29625

Sample Metadata Fields

Specimen part, Disease, Cell line

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accession-icon SRP128611
Pex3 deficiency effect on mouse testis
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Pex3 plays an essential role in peroxisomal membrane proteins (PMPs) import. Loss of Pex3 leads to a spermatogenic arrest.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Specimen part, Cell line

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accession-icon GSE97268
Genome-wide transcriptome analysis during differentiation of human embryonic stem (hES) cells into cardiac lineage
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

hES cells display an excellent model to study the developmental mechanisms occuring in vivo both at genetic and epigenetic levels. hES cell line were subjected to global transcriptome analysis to study the differentiation patterns during differentiation of pluripotent hES cells into cardic progenitors and beating cardiomyocytes.

Publication Title

No associated publication

Alternate Accession IDs

E-GEOD-97268

Sample Metadata Fields

Specimen part, Cell line, Time

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accession-icon SRP083126
Homo sapiens Transcriptome or Gene expression
  • organism-icon Homo sapiens
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Gene expression of Human THP-1 cells infected by cytomegalovirus

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Age, Specimen part

View Samples
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refine.bio is a repository of uniformly processed and normalized, ready-to-use transcriptome data from publicly available sources. refine.bio is a project of the Childhood Cancer Data Lab (CCDL)

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Cite refine.bio

Casey S. Greene, Dongbo Hu, Richard W. W. Jones, Stephanie Liu, David S. Mejia, Rob Patro, Stephen R. Piccolo, Ariel Rodriguez Romero, Hirak Sarkar, Candace L. Savonen, Jaclyn N. Taroni, William E. Vauclain, Deepashree Venkatesh Prasad, Kurt G. Wheeler. refine.bio: a resource of uniformly processed publicly available gene expression datasets.
URL: https://www.refine.bio

Note that the contributor list is in alphabetical order as we prepare a manuscript for submission.

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