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| Status |
Public on Dec 17, 2021 |
| Title |
SEM Rep1 |
| Sample type |
SRA |
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| Source name |
B-ALL cell line
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| Organism |
Homo sapiens |
| Characteristics |
b-all type: MLLr
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| Growth protocol |
Cells were grown in standard culture conditions with RPMI + 20% FBS and 1% pen-strep
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets were harvested in biological replicates and flash frozen. RNA was harvested using Qiagen Rneasy Kit. mRNA was purified from total RNA using Oligo (dT)25 magnetic beads ( NEB, S1550S)
Illumina sequencing library prep was performed using using KAPA Stranded RNAseq it with riboerase (Kapa Biosystems, KK8483)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
genes_FPKM.XLSX
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| Data processing |
Reads were mapped to the reference human (hg19) genome sequence, using Tophat2 aligner(Kim et al., 2013) with the default parameters.
The mRNA expression level for each gene was represented as FPKM, called by Cufflinks(Trapnell et al., 2010).
Genome_build: hg19
Supplementary_files_format_and_content: Excel file that includes FPKM for all samples
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| Submission date |
Dec 20, 2019 |
| Last update date |
Dec 17, 2021 |
| Contact name |
Matthew Nix |
| E-mail(s) |
matthew.nix@ucsf.edu
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| Organization name |
UCSF
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| Department |
Laboratory Medicine
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| Street address |
185 Berry St
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94107 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE142447 |
Surface proteomics reveals CD72 as a target for in vitro-evolved nanobody-based CAR-T cells in refractory B-cell malignancies I |
| GSE143181 |
Surface proteomics reveals CD72 as a target for in vitro-evolved nanobody-based CAR-T cells in refractory B-cell malignancies |
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| Relations |
| BioSample |
SAMN13656699 |
| SRA |
SRX7423357 |
| 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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