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Sample GSM2260194 Query DataSets for GSM2260194
Status Public on Mar 01, 2017
Title TT-seq 15min Rep2
Sample type SRA
Source name T cells
Organism Homo sapiens
Characteristics cell line: Jurkat cells
passage: 3-5
treatment: PMA + ionomycin
treatment duration: 15min
Treatment protocol Cells were labeled in media for 5 min with 500 μM 4-thiouridine (4sU, Sigma-Aldrich) and harvested through centrifugation for 2 min at 3,000 rpm.
Growth protocol Cells were grown in RPMI 1640 medium (Gibco) supplemented with 10% heat-inactivated FBS (Gibco) and 1% Penicillin/Streptomycin (100x, PAA) at 37°C under 5% CO2
Extracted molecule total RNA
Extraction protocol RNA was extracted using TRIzol (Life Technologies), 4sU-labeled RNA was exctracted according to Dolken et al., RNA, 2008.
fragmentation: yes; BioRuptor Next Gen (Diagenode) at high power for one cycle of 30’’/30’’ ON/OFF
sequencing libraries were prepared with the Ovation Human Blood RNA-seq library kit (NuGEN) following the manufacturer's’ instructions.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Description TT-seq
Data processing TT-seq and RNA-seq samples were mapped using STAR (version 2.3.0)
ChIP-seq reads were mapped with Bowtie (version 2.1.0) and duplicates were removed using PicardTools (version 1.118) MarkDuplicates.
Samtools was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f 163) were selected
PicardTools (version 1.118) CollectInsertSizeMetrics was used to determine average insert size and standard deviation with default settings: Deviations: 10.0; Minimum percentage: 0.05, Metric Accumulation Level: All reads
Genome_build: hg38 + Spikeins ERCC-00043, ERCC-00170, ERCC-00136, ERCC-00145, ERCC-00092 and ERCC-00002
Supplementary_files_format_and_content: gtf file contains the annotation used by us (available on the series record); bigwig files contain Coverage Files per sample (in case of RNAseq strand-specific antisense-corrected read coverage, in case of ChIP-seq not strand-specific, fragment coverage after duplicate removal)
Submission date Aug 04, 2016
Last update date May 15, 2019
Contact name Carina Demel
Organization name Max-Planck Institute for biophysical Chemistry
Street address Am Fassberg 11
City Göttingen
ZIP/Postal code 37077
Country Germany
Platform ID GPL18460
Series (1)
GSE85201 TT-seq captures simultaneous activation of eRNAs and promoters during T cell activation
BioSample SAMN05513104
SRA SRX2000726

Supplementary file Size Download File type/resource
GSM2260194_Jurkat_L_15min_2_GTCGTA.bam_antisenseCorrectedCoverage_crick.bigWig 1.2 Gb (ftp)(http) BIGWIG
GSM2260194_Jurkat_L_15min_2_GTCGTA.bam_antisenseCorrectedCoverage_watson.bigWig 1.2 Gb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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