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| Status |
Public on Oct 27, 2014 |
| Title |
OP9_DLL1_donor4 |
| Sample type |
SRA |
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| Source name |
CD34+, OP9-DLL1, donor4
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| Organism |
Homo sapiens |
| Characteristics |
co-culture: OP9-DLL1
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| Treatment protocol |
CD34+ thymocytes were purified out of pediatric thymus samples using MACS and seeded onto confluent OP9-GFP (control) or OP9-DLL1 plates for 48h in α-MEM media supplemented with 20% heat-inactivated FCS plus 100U penicilin, 100 µg/ml streptomycin, 2 mM L-glutamine and cytokines SCF, Flt-3 and IL-7 at 5 ng/ml each.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested with the miRNeasy mini kit (Qiagen) with Dnase treatment on-column.
RNA libraries were prepared for sequencing using standard Illumina protocols with poly-A enrichment
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
after QC with FastQC v0.10.1, reads were mapped to hg19 whole genome using tophat v2.0.10
A count file for each sample was generated using HTSeq-0.6.1 and Ensembl igenomes GTF file as reference.
Count files were merged into a count matrix and normalized in R using DESeq2
Differential expression analysis was done with DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normailzed count values for each Sample
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| Submission date |
Oct 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Annelynn Wallaert |
| E-mail(s) |
[email protected]
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| Organization name |
UGent
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| Street address |
De Pintelaan 185
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| City |
Gent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE62000 |
RNA-sequencing of CD34+ thymocytes that were cultured on an OP9-GFP or OP9-DLL1 feeder layer. |
| GSE62006 |
The Notch driven long non-coding RNA repertoire in T-cell acute lymphoblastic leukemia |
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| Relations |
| BioSample |
SAMN03092868 |
| SRA |
SRX719459 |
| 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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