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| Status |
Public on Mar 03, 2012 |
| Title |
BLM1Plus |
| Sample type |
SRA |
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| Source name |
45:30:25 mixture of brain, liver, and muscle RNA, respectively, with large dynamic concentration range of ERCC spike-in standards at 5 % of total RNA
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| Organism |
Homo sapiens |
| Characteristics |
cell type: 45:30:25 mixture of brain, liver, and muscle RNA, respectively, with large dynamic concentration range of ERCC spike-in standards at 5 % of total RNA
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| Extracted molecule |
total RNA |
| Extraction protocol |
Five micrograms of each total RNA plus spike sample was ribodepleted using the RiboMinus™ Human/Mouse Transcriptome Isolation Kit, Catalog Number K1550-01 (Invitrogen, Carlsbad, CA). Approximately 400 ng of ribodepleted RNA in solution was converted to cDNA libraries with SOLiD™ adaptors and barcodes, using the SOLiD™ Total RNA-Seq Kit, PN 4445374, and protocol PN4452437 Rev. A (Life Technologies, Carlsbad, CA). Ribodepleted RNA was enzymatically fragmented with RNase III using the stated protocol methods and assessed on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) with the RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA). Fragment distributions were found to have a median size of approximately 125 base pairs. SOLiD™ adaptors were then ligated onto the RNA and the RNA reverse transcribed. cDNA products were then amplified and uniquely barcoded using the SOLiD™ RNA Barcoding Kit, Modules 17-32 (Life Technologies, Carlsbad, CA). Following barcoding and amplification, completed cDNA libraries were assessed for size distribution and yield on the 2100 Bioanalyzer with the DNA 1000 Kit (Agilent Technologies, Santa Clara, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD 4 System |
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| 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:
101214_WT1_FC1_PE_Quad_1_BLM1_plus_bioscope_mapall_ERCCs_ercclowpur99skip50basepolyA_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
101214_WT1_FC1_PE_Quad_1_BLM1_plus_bioscope_mapall_hg18_dbsnp_132.hg18_reord_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
101214_WT1_FC1_PE_Quad_4_BLM1_plus_bioscope_mapall_ERCCs_ercclowpur99skip50basepolyA_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
101214_WT1_FC1_PE_Quad_4_BLM1_plus_bioscope_mapall_hg18_dbsnp_132.hg18_reord_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
101214_WT1_FC2_PE_Quad_1_BLM1_plus_bioscope_mapall_ERCCs_ercclowpur99skip50basepolyA_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
101214_WT1_FC2_PE_Quad_1_BLM1_plus_bioscope_mapall_hg18_dbsnp_132.hg18_reord_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
101214_WT1_FC2_PE_Quad_4_BLM1_plus_bioscope_mapall_ERCCs_ercclowpur99skip50basepolyA_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
101214_WT1_FC2_PE_Quad_4_BLM1_plus_bioscope_mapall_hg18_dbsnp_132.hg18_reord_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv: hg18
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| Submission date |
Mar 01, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Justin M Zook |
| E-mail(s) |
jzook@nist.gov
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| Phone |
3019754133
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| Organization name |
National Institute of Standards and Technology
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| Department |
Biochemical Science Division
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| Lab |
Material Measurement Laboratory
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| Street address |
100 Bureau Dr., MS8313
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| City |
Gaithersburg |
| State/province |
Maryland |
| ZIP/Postal code |
20899 |
| Country |
USA |
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| Platform ID |
GPL13393 |
| Series (1) |
| GSE36217 |
Comparison of systematic sequencing errors using spike-in standards |
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| Relations |
| SRA |
SRX124747 |
| BioSample |
SAMN00794508 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM883914_101214_WT1_FC1_PE_Quad_1_BLM1_plus_bioscope_mapall_ERCCs_ercclowpur99skip50basepolyA_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv.gz |
137.0 Kb |
(ftp)(http) |
CSV |
| GSM883914_101214_WT1_FC1_PE_Quad_1_BLM1_plus_bioscope_mapall_hg18_dbsnp_132.hg18_reord_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv.gz |
172.6 Kb |
(ftp)(http) |
CSV |
| GSM883914_101214_WT1_FC1_PE_Quad_4_BLM1_plus_bioscope_mapall_ERCCs_ercclowpur99skip50basepolyA_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv.gz |
156.2 Kb |
(ftp)(http) |
CSV |
| GSM883914_101214_WT1_FC1_PE_Quad_4_BLM1_plus_bioscope_mapall_hg18_dbsnp_132.hg18_reord_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv.gz |
192.6 Kb |
(ftp)(http) |
CSV |
| GSM883914_101214_WT1_FC2_PE_Quad_1_BLM1_plus_bioscope_mapall_ERCCs_ercclowpur99skip50basepolyA_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv.gz |
137.9 Kb |
(ftp)(http) |
CSV |
| GSM883914_101214_WT1_FC2_PE_Quad_1_BLM1_plus_bioscope_mapall_hg18_dbsnp_132.hg18_reord_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv.gz |
173.3 Kb |
(ftp)(http) |
CSV |
| GSM883914_101214_WT1_FC2_PE_Quad_4_BLM1_plus_bioscope_mapall_ERCCs_ercclowpur99skip50basepolyA_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv.gz |
158.9 Kb |
(ftp)(http) |
CSV |
| GSM883914_101214_WT1_FC2_PE_Quad_4_BLM1_plus_bioscope_mapall_hg18_dbsnp_132.hg18_reord_cov0_GATKbias_Dinuc_RemRefBias.table.recal_data.csv.gz |
193.1 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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