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| Status |
Public on Mar 01, 2017 |
| Title |
TT-seq 15min Rep1 |
| Sample type |
SRA |
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| Source name |
T cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: Jurkat cells
passage: 3-5
treatment: PMA + ionomycin
treatment duration: 15min
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| 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.
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| 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
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
TT-seq
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| 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)
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| Submission date |
Aug 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Carina Demel |
| E-mail(s) |
cdemel@mpibpc.mpg.de
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| Organization name |
Max-Planck Institute for biophysical Chemistry
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| Street address |
Am Fassberg 11
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| City |
Göttingen |
| ZIP/Postal code |
37077 |
| Country |
Germany |
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| Platform ID |
GPL18460 |
| Series (1) |
| GSE85201 |
TT-seq captures simultaneous activation of eRNAs and promoters during T cell activation |
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| Relations |
| BioSample |
SAMN05513105 |
| SRA |
SRX2000725 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2260193_Jurkat_L_15min_1_AAGCCT.bam_antisenseCorrectedCoverage_crick.bigWig |
158.1 Mb |
(ftp)(http) |
BIGWIG |
| GSM2260193_Jurkat_L_15min_1_AAGCCT.bam_antisenseCorrectedCoverage_watson.bigWig |
160.9 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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