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| Status |
Public on Apr 25, 2014 |
| Title |
CD49f-positive testicular cells |
| Sample type |
SRA |
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| Source name |
testicular cells
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| Organism |
Capra hircus |
| Characteristics |
cell type: primary testicular cell
strain: Saanen dairy goat
developmental stage: 5-month-old
cell surface markers: CD49f-positive
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| Treatment protocol |
Three testes from three 5-month-old dairy goats were collected and delivered back to the laboratory on ice, respectively. Then, the testicular cells were separated using CDD mixed digestive enzyme: 2 mg/mL collagenase (Invitrogen, Carlsbad, CA, USA) + 20 μg/ml DNase (Invitrogen) + 2 mg/ml decomposition enzyme (Invitrogen).Differential plating was performed to remove potential contamination of sertoli cells and myoid cells. The testicular cells were placed in a 10-cm diameter culture dish in DMEM/F12 medium supplemented with 10% FBS(Hyclone, Logan, UT, USA) at 37℃ overnight. Subsequently, the non-attached cells were collected for MACS by centrifuging at 1,000 rpm for 5 min.The CD49f-positive and negative testicular cells were obtained by MACS using a MiniMACS separation unit (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany).
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| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNAs of CD49f positive and negative testicular cells were extracted with RNAiso plus reagent (TaKaRa, Dalian, China) according to the manufacturer’s instructions,
A small RNA library was generated from the two RNA samples by the Illumina Truseq Small RNA Preparation kit according to Illumina’s TruSeq Small RNA Sample Preparation Guide.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina GAIIx following vendor’s instruction for running the instrument.
Raw sequencing reads were obtained using Illumina’s Sequencing Control Studio software version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70).
The extracted sequencing reads were stored in file and were then used in the sequencing data analysis.
The sequencing data analysis was analyzed using the ACGT101-miR v4.2 packages (LC Sciences, Houston, TX)
Genome_build: the latest release of miRBase (miRBase, http://www.mirbase.org/index.shtml), or genome based on the public releases of appropriate species. In this study, cattle and sheep were used as sequencing species for unique sequences to mirs, and goat was for unique sequences to genome
File contents and header definitions: See README_supplementary_file_contents.txt on Series record
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| Submission date |
Apr 24, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
wu jiang |
| E-mail(s) |
[email protected]
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| Organization name |
Northwest A&F University
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| Department |
College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology
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| Street address |
Taicheng road #3
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| City |
Yangling |
| State/province |
Shaanxi |
| ZIP/Postal code |
712100 |
| Country |
China |
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| Platform ID |
GPL15473 |
| Series (1) |
| GSE57041 |
The miRNA profiling of goat CD49f-positive and negative testicular cells |
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| Relations |
| BioSample |
SAMN02736807 |
| SRA |
SRX525993 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1373642_goat_CD49f+_testicular_cells_uni_miRs.txt.gz |
300.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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