|
| Status |
Public on Mar 01, 2013 |
| Title |
mix1-rep2 |
| Sample type |
SRA |
| |
|
| Source name |
placenta
|
| Organism |
Homo sapiens |
| Characteristics |
spike-in hsa-mir-147: 0.1
spike-in hsa-mir-211: 1
spike-in hsa-mir-219-5p: 10
spike-in hsa-mir-338-3p: 0.1
spike-in hsa-mir-383: 1
spike-in hsa-mir-429: 10
precursor spike-in hsa-mir-147: 0
o-methyl spike-in hsa-mir-211: 0
o-methyl spike-in hsa-mir-219-5p: 0
precursor spike-in hsa-mir-338-3p: 0
precursor spike-in hsa-mir-383: 0
o-methyl spike-in hsa-mir-429: 0
|
| Treatment protocol |
Oligos representing mature, modified and precursor miRNA were artificially introduced to native RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturer’s instructions. Briefly, 3` adapter was ligated to total RNA using RNL2, followed by 5’ adapter ligation, using T4 ligase. Reverse transcription with SuperScript II generated cDNA which was then PCR-amplified and size-selected on a gel and then purified. Sequencing was performed on two lanes of HiSeq 2000 using v2 clustering and sequencing reagents; seven libraries were multiplexed on each lane.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
fmol of spiked oligos per 1mg of total RNA
|
| Data processing |
Basecalls performed using CASAVA version 1.8.1
Adaptors were removed and then collapsed into tags and quantified.
Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).
The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against human mature miRNA databases (downloaded from mirbase.org, release 18).
The frequency of reads matching each miRNAs was calculated by summing the frequency of all the isoforms matching the miRNA
Genome_build: mirbase release 18
Supplementary_files_format_and_content: .txt file with rpm values for each miRNA
|
| |
|
| Submission date |
Sep 12, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Dena Leshkowitz |
| E-mail(s) |
dena.leshkowitz@weizmann.ac.il
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Bioinformatics Unit, Life Sciences Core Facilities
|
| Street address |
P.O.B. 26
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE40819 |
Differences in miRNA Detection Levels are Technology and Sequence Dependent [NGS] |
| GSE40820 |
Differences in miRNA Detection Levels are Technology and Sequence Dependent |
|
| Relations |
| SRA |
SRX186165 |
| BioSample |
SAMN01166099 |
