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| Status |
Public on Jul 01, 2012 |
| Title |
small RNA from red blood cells (Sample 1) |
| Sample type |
SRA |
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| Source name |
child
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| Organism |
Homo sapiens |
| Characteristics |
library number: library 1
tissue: red blood cell
developmental stage: child
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| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNA cDNA library was constructed using a protocol adapted from Hafner et al., 2008, Methods. Briefly total RNA from 9 individuals was size-fractionated via polyacrylamide gel electrophoresis and small RNAs corresponding in molecular weight to the mature miRNA population (15- 30-nucleotide fraction) were gel extracted. Small RNAs samples from the 4 healthy kids were pulled together to start with enough material. The 5 other samples were processed individually and all samples were then ligated to the 5' adaptor (Modban adenylated adaptor from IDT, San Jose, CA, USA) using the truncated RNL2 (NEB, Ipswich, MA, USA) and to a 3' adaptor (IDT, San Jose, CA, USA) sequentially using the T4 RNL1 (Promega, Dübendorf, Switzerland). The obtained cDNA samples were then RT-PCR amplified using the Superscript III Reverse transcriptase (Invitrogen AG, Basel, Switzerland) and Taq polymerase (Roche, Rotkreuz, Switzerland). The primers used for amplification included tails corresponding to the 454 adaptors and 3-nucleotide multiplexing tags. All samples were pulled into a single library for sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
454 GS FLX |
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| Description |
15-30 nucleotide small RNA
Small RNA from red blood cell from child donor
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| Data processing |
miRanalyzer (http://web.bioinformatics .cicbiogune.es/microRNA/miRanalyser.php)
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| Submission date |
Feb 11, 2011 |
| Last update date |
Jun 11, 2013 |
| Contact name |
imane azzouzi |
| Organization name |
Children's Hospital Zurich
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| Department |
Haematology division
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| Lab |
Erythrocyte Lab
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| Street address |
Steinwiesstrasse 75
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| City |
Zurich |
| ZIP/Postal code |
8032 |
| Country |
Switzerland |
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| Platform ID |
GPL9186 |
| Series (1) |
| GSE27250 |
Deep sequencing analysis of human red blood cells |
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| Relations |
| BioSample |
SAMN02197082 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM673700_library1.txt.gz |
23.9 Kb |
(ftp)(http) |
TXT |
| Processed data are available on Series record |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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