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| Status |
Public on Dec 09, 2015 |
| Title |
A_An_t1 |
| Sample type |
SRA |
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| Source name |
animal oocyte half
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| Organism |
Xenopus laevis |
| Characteristics |
cell type: oocyte
cell region: animal oocyte half
Stage: VI
oocytes taken from frog individual: A
animal/vegetal halves from batch: A_t1
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| Extracted molecule |
total RNA |
| Extraction protocol |
Oocyte halves were prepared by manual dissection, flash frozen in liquid nitrogen and RNA was prepared by proteinase K treatment, phenol-chloroform extraction and Lithiumchloride- as well as Ethanol/Ammoniumacetate-precipitation
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina Casava1.8.1 software used for basecalling.
Sequenced reads were mapped to transcript reference sequence (unique sequence for one gene id) for Xenopus tropicalis (source: Mike Gilchrist; http://genomics.nimr.mrc.ac.uk/resources/xenopus/Xt-transcripts-Xenbase-v72b-MJG-27oct11.fasta); using bowtie2 v2.1.0 with local alignment; 6MM for 50bp. We filled these sequences with annotation and took the longest sequence for one identifier (FullAnnotation5.csv).
Data was preprocessed and analyzed in the R environment (3.0.0) loading edgeR and biomaRt packages. Normalization, estimation of dispersions and testing for differentially expressed genes based on a test assuming negative binomial data distribution was computed via DESeq.
Genome_build: Xt72b [Collart C, Owens ND, Bhaw-Rosun L, Cooper B, De Domenico E, Patrushev I, Sesay AK, Smith JN, Smith JC, Gilchrist MJ. High-resolution analysis of gene activity during the Xenopus mid-blastula transition. Development. 2014 May;141(9):1927-39]
Supplementary_files_format_and_content: counts file includes normalized values for each sample
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| Submission date |
Jun 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Gabriela Salinas |
| E-mail(s) |
Gabriela.Salinas-Riester@medizin.uni-goettingen.de
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| Organization name |
Universitaetsmedizin Goettingen
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| Department |
Department of Pathology
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| Lab |
NGS Integrative Genomics
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| Street address |
Kreuzbergring 57
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| City |
Goettingen |
| State/province |
Lower-Saxony |
| ZIP/Postal code |
37075 |
| Country |
Germany |
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| Platform ID |
GPL17682 |
| Series (1) |
| GSE58420 |
Next generation sequencing identifies differentially localized transcripts in Xenopus laevis and Xenopus tropicalis oocytes |
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| Relations |
| BioSample |
SAMN02851412 |
| SRA |
SRX591681 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1410598_Sample_An10RNA_counts.txt.gz |
108.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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