|
| Status |
Public on Mar 27, 2015 |
| Title |
Fetal_2nd_2 |
| Sample type |
SRA |
| |
|
| Source name |
ovary from 2nd trimester embryos
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: multiple
oxidation: none
|
| Treatment protocol |
Oocytes, embryos and adult tissue were collected and stored at -80 until RNA extraction was performed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol (Ambion) according to manufacturer’s instruction. NaIO4 treatment was performed on RNA enriched for small RNA (mirVana, Ambion). For oxidation, RNA was exposed to 200mM NaIO4 in borate buffer (29.6mM borax, 29.6mM boric acid, pH6.8) for 10’/RT, then the reaction was stopped by the addition of glycerol. After precipitation with isopropanol and a 75% ethanol wash, libraries were prepared.
Library preparation was based on the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England BioLabs) with modifications. The 3’ and 5' adapters contained 4 random bases at the 5’- and 3’-end, respectively, and were chemically synthesized by BioScientific.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
TRIzol followed my miRVana (Ambion).
Total RNA enriched for molecules <200 nt.
Small RNA-Seq, strand-specific.
|
| Data processing |
Adapter sequences were clipped and the datasets were collapsed to non-identical cloning products (cliplinker_random.pl).
Sequences ranging from 18 to 34 nt were mapped to ncRNA datasets with SeqMap (version: 1.0.12).
Low complexity sequences were removed from the datasets (kill_simples.pl, default settings).
Sequences without annotation were mapped to the genome with piRmapper_1.0.pl (default settings).
Genome_build: Bos taurus: Bos_taurus_UMD_3.1, GenBank assembly accession GCA_000003055.3
Genome_build: Macaca fascicularis: Macaca_fascicularis_5.0, GenBank assembly accession GCA_000364345.1
Genome_build: Homo sapiens: GRCh38, GenBank assembly accession GCA_000001405.15
Supplementary_files_format_and_content: FASTA, sequence headers refer to read counts.
|
| |
|
| Submission date |
Jan 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
David Rosenkranz |
| E-mail(s) |
rosenkranz@uni-mainz.de
|
| Organization name |
Johannes Gutenberg-University Mainz
|
| Department |
Institute of Anthropology
|
| Street address |
Anselm-Franz-von-Bentzel-Weg 7
|
| City |
Mainz |
| ZIP/Postal code |
55099 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15520 |
| Series (1) |
| GSE64942 |
Piwi proteins and piRNAs in mammalian oocytes and early embryos |
|
| Relations |
| BioSample |
SAMN03283379 |
| SRA |
SRX840377 |
