|
| Status |
Public on Mar 03, 2012 |
| Title |
08-01-0277 |
| Sample type |
SRA |
| |
|
| Source name |
RNA extracted from B Lymphoblastoid cell lines established by Epstein-Barr Virus, with equimolar concentrations of ERCC spike-in standards at 5 % of total RNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: RNA extracted from B Lymphoblastoid cell lines established by Epstein-Barr Virus, with equimolar concentrations of ERCC spike-in standards at 5 % of total RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Rneasy Mini kit (Qiagen, MD). Fragmentation was performed using the Covaris S2AFA platform, and size selection of adapter-ligated cDNA was done using the Pippin Prep instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
The raw data was mapped using Bioscope v.1.3 (for SOLiD data) or bwa v.0.5.9 (for Illumina data) to hg18 with the ERCC spike-in sequences appended, using default mapping parameters. The BAM files were split into reads mapping to hg18 or to the spike-ins, and base quality score recalibration was done separately on these two files. To generate base quality score recalibration tables, GATK v.1.2-62 was used with the dbSNP v.132 vcf file for genome recalibration or ercclowpur99skip50basepolyA.vcf for spike-in standard recalibration.
Genome Build:
111014_08-01-0277_nopair_bwa_hg18_ERCConly_ercclowpur99skip50basepolyA_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
111014_08-01-0277_nopair_bwa_hg18_hg18only_dbsnp_132.hg18_reord_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
|
| |
|
| Submission date |
Mar 01, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Justin M Zook |
| E-mail(s) |
jzook@nist.gov
|
| Phone |
3019754133
|
| Organization name |
National Institute of Standards and Technology
|
| Department |
Biochemical Science Division
|
| Lab |
Material Measurement Laboratory
|
| Street address |
100 Bureau Dr., MS8313
|
| City |
Gaithersburg |
| State/province |
Maryland |
| ZIP/Postal code |
20899 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE36217 |
Comparison of systematic sequencing errors using spike-in standards |
|
| Relations |
| SRA |
SRX124749 |
| BioSample |
SAMN00794510 |
