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| Status |
Public on Mar 21, 2018 |
| Title |
Next-generation sequencing of matched ectopic and eutopic endometrium identifies novel endometriosis-related genes and highlights the role of general metabolism |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
AmpliSeq IonTorrent sequencing of mRNA derived from ectopic lesions and matched eutopic endometrium. There were 4 matched pairs overall; all donors were in mid-secretory phase.
[SUBMITTER_CITATION]:
A. V. Predeus, E. S. Vashukova, A. S. Glotov, M. M. Danilova, N. S. Osinovskaya, O. V. Malysheva, N. Yu. Shved, N. Ganbarli, M. I. Yarmolinskaya, T. E. Ivashchenko, V. S. Baranov - Next-Generation Sequencing of Matched Ectopic and Eutopic Endometrium Identifies Novel Endometriosis-Related Genes.
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| Overall design |
Each diluted library was amplified through emulsion PCR on Ion Sphere Particles (ISPs) using the Ion One Touch 200 Template kit with the Ion One Touch 2 system (Thermo Fisher Scientific, Inc.). Next, ISPs were recovered from the emulsion. Template-positive ISPs were enriched using Dynabeads MyOne Strepavidin C1 beads (Thermo Fisher Scientific, Inc.) by the OneTouch™ ES Instrument (Thermo Fisher Scientific, Inc.). ISP enrichment was confirmed by the Qubit 2.0 fluorimeter (Invitrogen, Carlsbad, CA, USA) using fluorescently labeled oligonucleotides complementary to adapter sequences. The enriched template-positive ISPs were loaded into Ion 318 Chip and sequenced on the Ion Torrent Personal Genome machine (Thermo Fisher Scientific, Inc.) using the Ion PGM Sequencing 200 Kit (Thermo Fisher Scientific, Inc.) according to the manufacturer's instructions.
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| Web link |
https://link.springer.com/article/10.1134/S1022795418110133
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| Contributor(s) |
Predeus AV, Vashukova ES, Glotov AS, Danilova MM, Osinovskaya NS, Malysheva OV, Shved NY, Yarmolinskaya MI, Ivaschenko TE, Baranov VS |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Jun 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexander Predeus |
| E-mail(s) |
predeus@gmail.com
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| Phone |
+447472882494
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| Organization name |
Wellcome Sanger Institute
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| Street address |
Wellcome Trust Genome Campus
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| City |
Hinxton |
| ZIP/Postal code |
CB10 1RQ |
| Country |
United Kingdom |
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| Platforms (1) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA390177 |
| SRA |
SRP109033 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE99949_EM_ampliseq.all_gene_DEseq2_norm.tsv.gz |
565.8 Kb |
(ftp)(http) |
TSV |
| GSE99949_EM_ampliseq.all_gene_rlog_norm.tsv.gz |
584.7 Kb |
(ftp)(http) |
TSV |
| GSE99949_EM_ampliseq.rsem.counts.tsv.gz |
13.5 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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