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| Status |
Public on Dec 15, 2017 |
| Title |
HoxB7cre_WT_SCR19 |
| Sample type |
SRA |
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| Source name |
Embryonic kidneys_wildtype
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| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL/6
tissue: kidneys
genotype: Control: Hnf1b+/fl
developmental stage: E15.5
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from microdissected kidneys was extracted by Tryzol using the miRNA mini kit Qiagen for extraction of total and miRNAs. The quality of the RNA samples was assessed on the Agilent Bioanalyzer system using the Agilent RNA 6000 Nano Kit (Agilent Technologies) and RNA with a Ring higher than 8 was used.
1-2 μg of total RNA were used for mRNA isolation using the Dynabeads® mRNA DIRECT™ Micro Kit (ThermoFisher Scientific).
mRNA was digested with RNase III, purified, hybridized and ligated to Ion Adaptors, reverse transcribed, barcoded and amplified, using the Ion Total RNA‐Seq Kit v2 (ThermoFisher Scientific).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
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| Description |
SCR19
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| Data processing |
RNA sequencing was performed on an Ion Proton™ System, according to the manufacturer's instructions.
The prepared libraries were quantified and pooled together in duplicates at the required concentration.
The library pools were then processed on an OneTouch 2 instrument and enriched on a One Touch ES station. Templating was performed using the Ion PI™ Template OT2 200 Kit (ThermoFisher Scientific) and sequencing with the Ion PI™Sequencing 200 Kit on Ion Proton PI™ chips (ThermoFisher Scientific) according to commercial protocols.
The resulting RNA-Seq BAM files were analyzed with the Bioconductor package metaseqR (Moulos and Hatsis, Nucleic Acids Res 43, e25 (2015) and applying the edgeR (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html) methodology for differential expression analysis with default settings.
Genome_build: mm9
Supplementary_files_format_and_content: Hoxb7 Hnf1b raw_counts_table.txt: raw counts of the 4 samples (SCR16, SCR17,SCR18,SCR19)
Hoxb7cre Hnf1b normalized_counts_table.txt: nrmalized counts of the 4 samples (SCR16, SCR17,SCR18,SCR19)
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| Submission date |
Oct 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Silvia Cereghini |
| E-mail(s) |
[email protected]
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| Phone |
331 44273137
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| Organization name |
IBPS- UMR7622 CNRS -UPMC
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| Department |
Developmental Biology
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| Lab |
Molecular Signaling
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| Street address |
9 Quai Saint Bernard BatC 7ET
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| City |
PARIS |
| ZIP/Postal code |
75005 |
| Country |
France |
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| Platform ID |
GPL18635 |
| Series (1) |
| GSE106085 |
HNF1B controls epithelial organization and cell polarity during ureteric bud branching and collecting duct morphogenesis |
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| Relations |
| BioSample |
SAMN07829500 |
| SRA |
SRX3316483 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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