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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 18, 2013 |
| Title |
SLE1-RNA-seq |
| Sample type |
SRA |
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| Source name |
primary monocytes
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| Organism |
Homo sapiens |
| Characteristics |
disease state: SLE patient
gender: Female
cell type: primary monocytes
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| Treatment protocol |
None
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| Growth protocol |
Primary monocytes
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 2-3 million purified primary monocytes using the Qiagen RNeasy kit and DNA was removed by on-column DNase digestion.
1 ug of total RNA was used to prepare the RNA seq libraries with the SOLiDTM whole transcriptome analysis kit (Applied Biosystems). The procedure followed the instructions of the manufacturer.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System 3.0 |
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| Data processing |
Build a colorspace Bowtie index, and align reads to hg19 using TopHat2
Assemble outputs of TopHat2 with Cufflinks 2.0.2, using RefSeq annotation as reference
Merge all the assemblies with CuffMerge
Create a reference Transcriptome based on CuffMerge output and a collection of non-coding RNAs, including lincRNA, small RNA, etc.
Run Novoalign to align reads again to the reference Transcriptome, and use the outputs to get read count mapped to each transcritpt
Genome_build: hg19
Supplementary_files_format_and_content: Excel file with multiple worksheet, each with a type of RNAs and their annotation
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| Submission date |
Dec 17, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kathleen E. Sullivan |
| E-mail(s) |
SULLIVANK@email.chop.edu
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| Phone |
2155901697
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| Organization name |
The Children's Hospital of Philadelphia
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| Department |
Immunology
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| Lab |
Sullivan
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| Street address |
3615 Civic Center Blvd.
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL9442 |
| Series (1) |
| GSE53419 |
The SLE transcriptome exhibits evidence of chronic endotoxin exposure and has widespread dysregulation of non-coding and coding RNAs |
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| Relations |
| BioSample |
SAMN02463198 |
| SRA |
SRX393481 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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