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| Status |
Public on Sep 13, 2023 |
| Title |
shGSK3a, 8h, vehicle |
| Sample type |
SRA |
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| Source name |
Jurkat
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| Organism |
Homo sapiens |
| Characteristics |
cell line: Jurkat
cell type: T-ALL cells
genotype: shGSK3a
timepoint: 8h
treatment: veh
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| Treatment protocol |
Cells were treated with vehicle or 100 U/L asparaginase at indicated timepoints before harvesting.
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| Growth protocol |
Cells were maintained in RPMI 1640 (Thermo Fisher Scientific) with 10% fetal bovine serum (FBS, Sigma-Aldrich, Saint Louis, MO) and 1% penicillin/streptomycin (Thermo Fisher Scientific) at 37°C, 5% CO2.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated at indicated time points using the RNeasy kit (Qiagen) according to the manufacturer’s protocols.
Library preparation was performed by eurofins genomics
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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 |
Initial quality control of transcriptomics data was performed using FastQC version 0.11.9
“filter by tile” function of BBMap was used to discard low-quality reads
trimming with trimmomatic version 0.39 using specifications: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True HEADCROP:14 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Orphaned reads were merged to their respective paired fastq files using the cat command of Ubuntu 22.04.1 LTS
Preprocessed reads were mapped using kallisto version 0.46.1 with a transcriptome index created using homo sapiens Ensembl v108 GRCh38.p13
Transcripts of genes with an associated HGNC accession were categorized as protein-coding or non-protein-coding using Ensembl gene biotype information. Transcripts with labels "IG_C_gene", "IG_D_gene", "IG_V_gene", "IG_J_gene", "protein_coding", "TR_D_gene", "TR_J_gene", "TR_V_gene" were considered as protein coding.
Counts with a count < 10 across all analyzed samples were discarded for transcripts.
The remaining transcripts were normalized to obtain transcript per million (TPM) values.
TPMs of transcripts associated with the same HGNC accession were added up to calculate gene level expression. On the gene level, a zTPM cut-off was used to exclude lowly expressed genes and their transcripts (T. Hart, H. K. Komori, S. LaMere, K. Podshivalova, and D. R. Salomon, "Finding the active genes in deep RNA-seq gene expression studies," (in eng), BMC genomics, vol. 14, p. 778, Nov 11 2013, doi: 10.1186/1471-2164-14-778.).
Assembly: homo sapiens Ensembl v108 GRCh38.p13
Supplementary files format and content: table in tab-separated values formating including kallisto estcount, as well as TPM and log2FC for the samples
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| Submission date |
Jun 13, 2023 |
| Last update date |
Sep 13, 2023 |
| Contact name |
Laura Hinze |
| E-mail(s) |
hinze.laura@mh-hannover.de
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| Organization name |
Hannover Medical School
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| Street address |
Carl-Neuberg-Straße 1
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| City |
Hannover |
| State/province |
Niedersachsen |
| ZIP/Postal code |
30625 |
| Country |
Germany |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE234800 |
Identifying early, intermediate, and late responses to GSK3a inhibition in Jurkat T-ALL cells in the presence or absence of an asparagine depletion |
| GSE234803 |
Amino acid availability is a crucial factor for survivability of cancer cells |
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| Relations |
| BioSample |
SAMN35725386 |
| SRA |
SRX20671633 |
| 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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