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| Status |
Public on Jun 17, 2023 |
| Title |
HUVEC, treated, 6h, biol rep 3 |
| Sample type |
SRA |
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| Source name |
HUVEC
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HUVEC
cell type: endothelial cells
treatment: CEA-TCB
timepoint: 6h
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| Treatment protocol |
HUVECs were incubated with superntants from T cell dependent cytotoxicity assay with CEA-TCB or DP47-TCB (untargeted-TCB) for 6 hrs.
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| Extracted molecule |
total RNA |
| Extraction protocol |
At assay endpoint (6hrs), HUVECs were washed with PBS, lysed with 350 µL of RTL buffer, and frozen at -80°C prior the RNA extraction following manufacturer’s instructions (QIAGEN RNeasy Mini Kit).
The RNA concentration was quantified using a Nanodrop instrument and the quality of the preparations (RIN) was evaluated with an Agilent BioAnalyzer. Libraries were prepared using Illumina TruSeq Stranded mRNA kit following the recommended instructions and quantified using qPCR KAPA Library Quantification kit (KAPA Biosystems). The fragment size distribution was evaluated using an Agilent Tapestation. The libraries were sequenced in an Illumina NovaSeq6000 instrument (R1:51, i7:8, i5:8, R2:51) with a targeted depth of 30 Mio paired reads per sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
s6
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| Data processing |
RNA-seq reads were quantified using Kallisto v0.46.1 and human reference transcriptome from ENSEMBL r107.
Transcript-level estimates of counts and tpm were imported and summarized at the gene-level using tximport v1.26.1 from Bioconductor.
Assembly: GRCh38.p13
Supplementary files format and content: Supplementary file raw_count.csv provides estimated counts obtained from Kallisto, rounded to the smallest successive integer. Rows are ENSEMBL Gene IDs and columns are individual samples.
Supplementary files format and content: Supplementary file raw_tpm.csv provides tpm values obtained from Kallisto. Rows are ENSEMBL Gene IDs and columns are individual samples.
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| Submission date |
Jun 12, 2023 |
| Last update date |
Jun 17, 2023 |
| Contact name |
Marina Bacac |
| Organization name |
Roche Glycart AG
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| Department |
Oncology Discovery
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| Street address |
Wagistrasse 10
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| City |
Schlieren |
| ZIP/Postal code |
8952 |
| Country |
Switzerland |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE234668 |
Dissecting the mechanisms underlying the Cytokine Release Syndrome (CRS) mediated by T Cell Bispecific Antibodies |
| GSE234676 |
Dissecting the mechanisms underlying the Cytokine Release Syndrome (CRS) mediated by T Cell Bispecific Antibodies |
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| Relations |
| BioSample |
SAMN35713947 |
| SRA |
SRX20657781 |
| 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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