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Sample GSM6726608 Query DataSets for GSM6726608
Status Public on Nov 10, 2023
Title U937 cells, non-targeting control, rep 1
Sample type SRA
 
Source name U-937
Organism Homo sapiens
Characteristics cell line: U-937
cell type: Monocytes
disease: Acute Myeloid Leukemia
genotype: Non-targeting control
treatment: CRISPR sgRNA lentiviral transduction
Treatment protocol Cells were transduced with CRISPR sgRNA lentivirus targeting MLL, CSNK2A1, SGF29 or non-targeting control. Puromycin (1ug/ul) was added 2 days after to select for transduced cells and removed from the culture upon selection completion.
Cells were harvested by centrifugation 7 days after puromycin removal and washed with 1X PBS and protease inhibitors.
Growth protocol Cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum, 2mM Glutamine and 100 U/ml penicillin/streptomycin in a humidified atmosphere with 5% CO2 at 37C.
Extracted molecule polyA RNA
Extraction protocol RNA was extracted using the Rneasy Mini Kit (Qiagen) and 900ng of total RNA per sample were used for library preparation.
RNA library prep was performed with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) follownig the manufacturer's instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description NTC1
TPM_MLL-CK2-NTC.xlsx
Data processing Raw reads were preprocessed by trimming Illumina Truseq adapters, polyA, and polyT sequences using cutadapt v2.3 with parameters “cutadapt -j 4 -m 20 --interleaved -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT Fastq1 Fastq2 | cutadapt --interleaved -j 4 -m 20 -a "A{100}" -A "A{100}" - | cutadapt -j 4 -m 20 -a "T{100}" -A "T{100}" -”.
Trimmed reads were subsequently aligned to human genome version hg38 using STAR aligner v2.7.0d_0221 with parameters according to ENCODE long RNA-seq pipeline.
Gene expression levels were quantified using RSEM v1.3.1. Ensembl v84 gene annotations were used for the alignment and quantification steps. RNA-seq sequence, alignment, and quantification qualities were assessed using FastQC v0.11.5 and MultiQC v1.8. Lowly expressed genes were filtered out by retaining genes with estimated counts (from RSEM) ≥ number of samples times 5.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.
 
Submission date Nov 10, 2022
Last update date Nov 10, 2023
Contact name Karina Ofelia Barbosa Guerra
E-mail(s) karinabarbosa4@gmail.com, adeshpande@sbpdiscovery.org
Organization name Sanford Burnham Prebys Medical Discovery Institute
Department Tumor Initiation & Maintenance Program
Lab Deshpande
Street address 10901 North Torrey Pines Rd, Deshpande Lab RM6210B
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL18573
Series (2)
GSE217776 Effect of CRISPR knockout of MLL, CSNK2A1 and SGF29 on gene expression profiles in acute myeloid leukemia U937 cells [RNA-seq]
GSE217829 Epigenetic regulator landscape of HOX/MEIS expression in AML
Relations
BioSample SAMN31687123
SRA SRX18235699

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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