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Sample GSM4227035 Query DataSets for GSM4227035
Status Public on May 29, 2020
Title Hit4_rep3
Sample type SRA
 
Source name chronic myelogenous leukemia (CML) cell line
Organism Homo sapiens
Characteristics cell line: KBM7 Cancer Cell Line
disease: CML
treatment: Hit4
Treatment protocol KBM7 cells treated for 5h with DMSO, dCeMM-1, dCeMM-2, dCeMM-3, dCeMM-4 (10xEC50) and THZ531 (600nM). Triplicates per condition.
Growth protocol IMDM 10%FBS 1%P/S
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
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"
 
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
Organization name CeMM, Vienna
Street address Lazarettgasse 14, AKH BT 25.3
City Vienna
ZIP/Postal code 1090
Country Austria
 
Platform ID GPL21290
Series (1)
GSE142405 Rational and scalable strategies to identify small “molecular glue” degraders
Relations
BioSample SAMN13648532
SRA SRX7419894

Supplementary file Size Download File type/resource
GSM4227035_Hit4_rep3_read_counts.txt.gz 193.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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