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| Status |
Public on May 29, 2020 |
| Title |
DMSO_rep3 |
| Sample type |
SRA |
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| Source name |
chronic myelogenous leukemia (CML) cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: KBM7 Cancer Cell Line
disease: CML
treatment: DMSO
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| Treatment protocol |
KBM7 cells treated for 5h with DMSO, dCeMM-1, dCeMM-2, dCeMM-3, dCeMM-4 (10xEC50) and THZ531 (600nM). Triplicates per condition.
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| Growth protocol |
IMDM 10%FBS 1%P/S
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted with the RNeasy mini kit (Qiagen 74106). To account for global differences in transcriptional output, an exogenous spike-in approach was employed, according to the manufacturer's protocol (SIRV-Set 3 Iso Mix E0 / ERCC from Lexogen, Cat. No 051). RNA amount was determined using the Qubit RNA HS Kit (Thermo, Q32852).
CORALL Total RNA-Seq Library Prep Kit (Lexogen, #095.24), poly-A enrichment.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
conversion and demultiplexing: IlluminaBasecallsToMultiplexSam to generate one bam file per lane from the data on the Illumina machine, IlluminaSamDemux to demultiplex the bam file into multiple samples (https://github.com/DanieleBarreca/picard)
trimming: Trimmomatic (version 0.32) using the following parameters: HEADCROP:13 ILLUMINACLIP:epignome_adapters_2_add.fa:2:10:4:1:true SLIDINGWINDOW:4:1 MAXINFO:16:0.40 MINLEN:18
alignment: STAR aligner version 2.5.2b
defining genes: genome-build GRCh38.p7, genome-build-accession NCBI:GCA_000001405.22. Additionally, sequences and annotations in FASTA and GTF format for SIRV Set 3 (SIRV Isoform Mix E0 and ERCCs, Cat. No 051) included in SIRV_Set3_Sequences_170612a (ZIP) were downloaded from https://www.lexogen.com/sirvs/download/
read counts files: htseq-count (version 0.11.2) from the HTSeq framework
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: tab-delimited text files include raw read counts mapped to genes from the human genome and artificial "SIRVome"
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| Submission date |
Dec 20, 2019 |
| Last update date |
May 30, 2020 |
| Contact name |
Hana Imrichova |
| E-mail(s) |
hana.imrichova@gmail.com, himrichova@cemm.oeaw.ac.at
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| Organization name |
CeMM, Vienna
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| Street address |
Lazarettgasse 14, AKH BT 25.3
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| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
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| Platform ID |
GPL21290 |
| Series (1) |
| GSE142405 |
Rational and scalable strategies to identify small “molecular glue” degraders |
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| Relations |
| BioSample |
SAMN13648541 |
| SRA |
SRX7419884 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4227026_DMSO_rep3_read_counts.txt.gz |
184.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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