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| Status |
Public on May 21, 2019 |
| Title |
KO820 |
| Sample type |
SRA |
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| Source name |
lateral ventricle and Choroid plexus from Mus musculus strain C57BL/6J
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: lateral ventricles and Choroid plexus
developmental stage: adult
genotype/variation: TAp73 Knock-out
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| Extracted molecule |
total RNA |
| Extraction protocol |
Phenol/Chloroform total RNA isolation.
TruSeq Illumina small-RNA sequencing (according to manufacture recommendations)
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
p404sKO820
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| Data processing |
Base-calling
bcl2fastq v2.17.1.14
Adapter trimming, alignment, novel miRNA detection and read counting
Oasis 2 module 1 (sRNA detection)
https://oasis.dzne.de/
Differential expression analysis
Oasis 2 module 2 (DE analysis)
https://oasis.dzne.de/small_rna_de.php
Genome_build: mm10
Supplementary_files_format_and_content: Counts
DE_genes.xls and DE_genes_min5reads.xls, they both contain differential expression analysis of wild-type vs. knock-out samples generated with Oasis 2 module 2 (DE analysis) (Capece, Vincenzo, et al. "Oasis: online analysis of small RNA deep sequencing data." Bioinformatics 31.13
(2015): 2205-2207, https://oasis.dzne.de/small_rna_de.php), where DE_genes.xls contains the results for all small RNAs (sRNAs), and DE_genes_min5reads.xls contains the results for sRNAs with at least 5 raw reads on average in either condition (i.e. sRNAs with less than 5 reads on average in both conditions are filtered out). As for the contents of both files, those are as follows:
1) mature - accession ID of sRNA
2) structure - indication of the type of sRNA: micro (miRNA), novel micro, piwi-related (piRNA), ribosomal (rRNA), small nucleolar (snoRNA) or small nuclear (snRNA)
3) sRNA coordinates (4 columns containing chromosome name, start and stop positions and strand); entries of "multiple" indicate family of sRNAs associated with multiple genomic coordinates
4) Differential expression statistics, including log2FoldChange, adjusted p-value (padj), overall baseMean, base mean for wild-type samples only (baseMean_control) and for knock-out samples only (baseMean_treatment_files_1), log2 fold-change standard error (lfcSE), statistic score used by DESeq2 to calculate the p-values (stat), and the original pvalue
5) Normalised read counts for each sample (p404sWT817_Lize_S70_L008, p404sWT819_Lize_S72_L008, and p404sWT827_Lize_S73_L008 for the wild- type samples, and treatment_files_1_p404sKO818_Lize_S71_L008,
treatment_files_1_p404sKO820_Lize_S67_L008,
treatment_files_1_p404sKO832_Lize_S68_L008 and
treatment_files_1_p404sKO833_Lize_S69_L008 for the knock-out samples).
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| Submission date |
Dec 21, 2017 |
| Last update date |
May 21, 2019 |
| Contact name |
Gabriela Salinas |
| E-mail(s) |
[email protected]
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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 |
GPL21103 |
| Series (1) |
| GSE108385 |
TAp73 functions through posttranscriptional codes in brain multiciliogenesis |
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| Relations |
| BioSample |
SAMN08223788 |
| SRA |
SRX3502480 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2897079_p404sKO820_Lize_S67_L008_allspeciesCounts.txt.gz |
264.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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