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Sample GSM4141990 Query DataSets for GSM4141990
Status Public on May 11, 2020
Title PRO-seq_MJ-19-30_MED14-dTAG_2h_dTAG7_B
Sample type SRA
 
Source name PRO-seq_MJ-19-30_MED14-dTAG_2h_dTAG7
Organism Homo sapiens
Characteristics cell line: KBM7
cell type: chronic myeloid leukemia cell line
genotype/variation: MED14-dTAG
treatment: 2h 500nM dTAG7
experiment id: MJ-19-30
molecule subtype: nuclear RNA
Treatment protocol 60mio cells were treated for 0.5-2h with 500nM dTAG7, 500nM NVP2, or DMSO and 5% Drosophila S2 cells added for cross-normalization before extracting nuclei on ice.
Growth protocol KBM7 cells were grown in IMDM medium supplemented with 10% FBS and 1% Pen/Strep.
Extracted molecule total RNA
Extraction protocol PRO-seq libraries were generated as previously described (PMID: 27442863), with 4 parallel run-on reactions per sample. Total RNA was merged after the first RNA precipitation step.
Library construction by PCR amplification with custom primers.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 3000
 
Description cross-compare only to MJ-19-30 samples
Data processing library strategy: PROT-seq
conversion and demultiplexing: Illumina2bam
FASTQ conversion: bamtools v2.3.0 convert -format fastq
trimming: cutadapt v1.9.1 -a "TGGAATTCTCGGGTGCCAAGG" --minimum-length=10
reverse_complement: fastx_reverse_complement v0.0.14
alignment: 'bowtie v2.2.9 --very-sensitive' to a fused index of hg38_dm6_rDNA-U13369; later filtered with 'samtools v1.7 view -q 20'
spike-in_counting: number of reads aligning to dm6 were counted with "samtools view | awk '$3 ~ /dm6_/ {++dm6_count}'" and normalization factor alpha=1e6/dm6_count (see PMID: 25437568)
signal_trimming_to_3prime_base: only 3' base (Pol II active center) was retained in BED files with "bedtools v2.26.0 bamtobed | awk '($6 == "+") {print $1,$3-1,$3,$4,$5,$6}; ($6 == "-") {print $1,$2,$2+1,$4,$5,$6}'"
Genome_build: hg38
Supplementary_files_format_and_content: bigWig generation: spike-in normalized, strand-specific signal tracks were computed with 'bedtools v2.26.0 genomeCoverageBed -bg -strand -scale $alpha' followed by UCSC 'bedGraphToBigWig v4'
 
Submission date Oct 28, 2019
Last update date May 12, 2020
Contact name Georg E Winter
Organization name CeMM - Research Institute for Molecular Medicine of the Austrian Academy of Sciences
Street address Lazarettgasse 14, AKH BT25.3
City Wien
State/province Austria
ZIP/Postal code 1090
Country Austria
 
Platform ID GPL21290
Series (2)
GSE139462 Selective Mediator-dependence of cell type-specifying transcription [PRO-seq]
GSE139468 Selective Mediator dependence of cell-type-specifying transcription
Relations
BioSample SAMN13139743
SRA SRX7064242

Supplementary file Size Download File type/resource
GSM4141990_MJ-19-30_dTAG7_2h_B_minus_dm6_normalized.bw 79.2 Mb (ftp)(http) BW
GSM4141990_MJ-19-30_dTAG7_2h_B_plus_dm6_normalized.bw 81.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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