|
Status |
Public on Sep 08, 2013 |
Title |
wt Thymus rep2B |
Sample type |
SRA |
|
|
Source name |
Whole Thymus
|
Organism |
Mus musculus |
Characteristics |
strain: wt_c57BL/6 tissue: Thymus age: 4_week
|
Growth protocol |
Single cell suspensions were prepared from whole thymus of 4 week old mice.
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Cell suspensions were prepared from 4 week old whole thymus and filtered through 70 m nylon cell strainer (BD Biosciences). RNA was prepared by the use of TRI Reagent (Molecular Research Center, Inc.) followed by purification using RNeasy kit (Qiagen) with on-column RNase-free DNase I treatment. For RNA-Seq analysis, cDNA library was prepared for the Illumina Sequencing platform using the fragmented double-stranded cDNA protocol (Nagalakshmi et al., 2010), and sequenced on an Illumina GAIIx machine with 76 bp single-end reads (replicate 1) or on an Illumina HiSeq machine with 50 bp single-end reads at the Broad Stem Cell Research Center High Throughput Sequencing Core at UCLA.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
Raw data was uploaded to the Galaxy website (http://galaxy.psu.edu/) and mapped with Tophat to the July 2007 annotation of mouse (Mus musculus) genome data (mm9), filtering for uniquely mapped reads (Blankenberg et al., 2010; Goecks et al., 2010). Genome coverage visualization files were created in Galaxy (replicate 1) or with BEDtools (replicate 2) and uploaded to the UCSC genome browser (http://genome.ucsc.edu) (Kent et al., 2002). Tophat alignment through Galaxy resulted in .sam and .bedgraph files.
|
|
|
Submission date |
Sep 16, 2011 |
Last update date |
May 15, 2019 |
Contact name |
Hilde Schjerven |
Organization name |
UCSF
|
Department |
Laboratory Medicine
|
Street address |
513 Parnassus Ave
|
City |
San Francisco |
State/province |
CA |
ZIP/Postal code |
94143 |
Country |
USA |
|
|
Platform ID |
GPL13112 |
Series (2) |
GSE32190 |
Selective Functions of Individual Zinc Fingers Within the DNA-Binding Domain of Ikaros (RNA-seq: Thymocytes) |
GSE33693 |
Selective Functions of Individual Zinc Fingers Within the DNA-Binding Domain of Ikaros |
|
Relations |
Reanalyzed by |
GSE80797 |
SRA |
SRX097649 |
BioSample |
SAMN00722027 |
Named Annotation |
GSM797706_wt_2B_Thym.bigwig |