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| Status |
Public on Jun 01, 2014 |
| Title |
Total smRNA-seq |
| Sample type |
SRA |
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| Source name |
Testis
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| Organism |
Callithrix jacchus |
| Characteristics |
tissue: Testis
age: 41 month
genotype: Wild Type
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| Extracted molecule |
total RNA |
| Extraction protocol |
Testis was dissected and frozen. For MARWI-IP samples, immunoprecepitation of MARWI was performed using testis lysates followed by RNA isolation using miRNeasy kit (Qiagen, 217004). For small RNA-seq samples, RNA was harvested from the testes using miRNeasy kit (Qiagen, 217004), and the size fractionation was obtained by gel-purification from total RNA, using the Small RNA Gel Extraction kit (TaKaRa, RR065). RNA-seq samples were prepared by total RNA isolation using miRNeasy kit (Qiagen, 217004).
small RNA-seq libraries were prepared using NEBNext Small RNA Library Sample Prep Set (New England BioLabs (NEB), E7330), and RNA-seq libraries were prepared with the directional mRNA-seq library prep protocol using the TruSeq Small RNA Sample Prep Kit (Illumina, RS-200-0012).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
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| Data processing |
small RNA-seq and MARWI-IP-seq: Adapter sequences were removed from obtained reads, and mapped to the marmoset reference genome (calJac3, WUSTL 3.2) using Bowtie (Langmead et al., 2009) allowing zero mismatches. Annotation of the reads was determined according to UCSC genome browser (Meyer et al., 2013) and Ensembl databases (Flicek et al., 2013).
RNA-seq: Adapter sequences were removed, and the reads were mapped to the marmoset reference genome (calJac3, WUSTL 3.2) using Bowtie (Langmead et al., 2009) with default parameters. Expression of each transcript was determined using TopHat (Trapnell et al., 2009) and Cufflinks (Trapnell et al., 2010), except for Argonaute proteins as these sequences were unavailable within the Ensembl data (C_jacchus3.2.1) (Flicek et al., 2013). We determined the expression of marmoset Argonaute/Piwi mRNAs by calculating the number of reads that uniquely map to the transcript sequence of each Argonaute/Piwi mRNA. These mapped reads were normalized by the length of each transcript and the total number of genome mapped reads to calculate Reads pre Kilobase per Million mapped reads (RPKM).
Genome_build: WUGSC 3.2/calJac3
Supplementary_files_format_and_content: tab-delimited text files include sequences and their read counts for genome-mapped small RNA-seq sample (smRNA-seq_smRNAreads.txt); tab-delimited text files include read counts for genome-mapped MARWI-IP small RNA-seq samples (MARWI-IP_seq_smRNAreads.txt); tab-delimited text files include RPKM values for RNA-seq samples (RNAseq_RPKM.txt).
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| Submission date |
Dec 03, 2013 |
| Last update date |
Jul 03, 2021 |
| Contact name |
Yuka W. Iwasaki |
| E-mail(s) |
iwasaki@keio.jp
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| Organization name |
Keio University School of Medicine
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| Department |
Department of Molecular Biology
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| Lab |
Siomi Lab
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| Street address |
35 Shinanomachi, Shinjuku-ku,
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| City |
Tokyo |
| ZIP/Postal code |
160-8582 |
| Country |
Japan |
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| Platform ID |
GPL18020 |
| Series (1) |
| GSE52927 |
Small RNA and gene expression profile in the adult testes of the common marmoset |
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| Relations |
| BioSample |
SAMN02429366 |
| SRA |
SRX386263 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1278256_smRNA-seq_smRNAreads.txt.gz |
24.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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