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Status |
Public on May 24, 2023 |
Title |
HEL Mmb 48h - 1 |
Sample type |
SRA |
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Source name |
HEL
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Organism |
Homo sapiens |
Characteristics |
cell line: HEL treatment: Momelotinib
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA from cell lines was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) with DNAse treatment following the manufacturer's protocol. Samples were then indexed, pooled, and sequenced by Illumina NovaSeq 6000 following standard Illumina protocol.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Data processing |
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a. TMM normalization size factors in EdgeR were calculated to adjust for samples for differences in library size. Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis. Assembly: GrCh38 Supplementary files format and content: TSV of raw counts.
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Submission date |
Apr 14, 2023 |
Last update date |
May 24, 2023 |
Contact name |
Tim Kong |
E-mail(s) |
timkong@wustl.edu
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Organization name |
Washington University School of Medicine
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Street address |
CSRB 8838
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City |
St. Louis |
State/province |
MO |
ZIP/Postal code |
63110 |
Country |
USA |
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Platform ID |
GPL24676 |
Series (1) |
GSE229712 |
Comprehensive profiing of clinical JAK inhibitors in myeloproliferative neoplasms |
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Relations |
SRA |
SRX19970726 |
BioSample |
SAMN34179464 |
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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