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| Status |
Public on Aug 01, 2012 |
| Title |
Ago4 mRNAAgo4 WT Day3 |
| Sample type |
SRA |
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| Source name |
Day 3 Whole Testis
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| Organism |
Mus musculus |
| Characteristics |
age: 3 days
strain: C57BL/6
genotype: Ago4+/+
tissue: testis
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were removed or isolated and homogenized. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001, FC-122-1002) was used with 2 ug of total RNA for the construction of sequencing libraries.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
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| Data processing |
mRNA
Data were filtered using Illumina's automated quality filter. Low quality bases were also trimmed using custom software.
Reads were aligned to the transcriptome using TopHat (v1.3.0).
Differential expression between paired wild-type and knock-out samples was determined using Cuffdiff, a sub-package of Cufflinks (v1.1.0).
small RNA
Data was filtered to remove reads shorter than 14 nucleotides, lacking the proper cloning adapters sequence, and containing low quality bases (bases called as 'N').
Sequences were aligned to genome using Bowtie (v0.12.7).
Genome matching reads were aligned to hairpins from miRBase (release 18).
Genome_build: Mus Musculus NCBI Build 37
Supplementary_files_format_and_content: Cuffdiff (a sub-package of Cufflinks) differential expression spreadsheet, containing, for each gene, RPKM values for wild-type (sample_2) and AGO4 knock-out (sample_1) samples.
Supplementary_files_format_and_content: All sequenced reads in the format of a non-redudnant list of unique sequences, followed by the number of times each sequence appeared in wild-type (columns 1 and 2) and AGO4 knock-out (columns 3 and 4) mouse small RNA libraries.
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| Submission date |
Jul 25, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephanie Renee Hilz |
| E-mail(s) |
stephanie.hilz@gmail.com
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| Organization name |
Cornell University
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| Street address |
Biotech 445, Cornell University
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| City |
Ithaca |
| ZIP/Postal code |
14850 |
| Country |
USA |
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| Platform ID |
GPL15103 |
| Series (1) |
| GSE39652 |
AGO4 Regulates Entry into Meiosis and Influences Silencing of Sex Chromosomes in the Male Mouse Germline |
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| Relations |
| SRA |
SRX170901 |
| BioSample |
SAMN01094253 |
| 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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