|
Status |
Public on Apr 26, 2018 |
Title |
ssrp1_TSS-Seq_rep1 |
Sample type |
SRA |
|
|
Source name |
Whole seedlings
|
Organism |
Arabidopsis thaliana |
Characteristics |
ecotype: Columbia (Col-0) tissue: Whole seedlings genotype: ssrp1-2/ssrp1-2 age: 14 day
|
Growth protocol |
The Arabidopsis seedlings were grown on plates (1/2 Murashige and Skoog medium, 1% sucrose, 0.5% Microagar) with a 16h light/8h dark cycle at 22°C.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated from 14 day old seedlings using QIAgen Plant RNeasy Mini Kit following manufacturer’s instructions TSS-Seq: libraries were prepared as described in Pelechano et al. Nat Protoc. 2016 Feb 11(2):359-76; PMID: 26820793. RNA-Seq: libraries were prepared using Illumina TruSeq Sample Prep Kit v2 following the manufacturer's protocol.
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Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
Library strategy: TSS-Seq Illumina Casava v1.7 software was used for basecalling. TSS-Seq: 1) Adapter trimming (Trim Galore v0.4.3; --adapter "ATCTCGTATGCCG"); 2) Trim UMI barcodes (8 nt; UMI-Tools extract); 3) Alignment (STAR v2.5.2b; --outSAMmultNmax 1 --alignEndsType Extend5pOfRead1); 4) Sort BAM files (Samtools v1.3.1); 5) Remove reads aligned to rRNA, tRNA, snRNA or snoRNA loci (BEDTools v2.17.0); 6) Remove reads with MAPQ < 10 (Samtools v1.3.1); 7) Deduplication (UMI-Tools dedup); 8) Make stranded bedGraph files from the 5' bases (BEDTools genomecov; -bg -5 -strand + / -); 9) Remove singletons (awk) and convert to Bigwig (kentUtils bedGraphToBigWig). See the full pipeline in https://github.com/Maxim-Ivanov/Nielsen_et_al_2018/01-Alignment_of_5Cap-Seq_data.sh RNA-Seq: 1) Adapter trimming (Trim Galore v0.4.3; --paired --illumina); 2) Alignment (STAR v2.5.2b; --outSAMmultNmax 1 --alignEndsType Local); 3) Sort BAM file, remove reads with MAPQ < 10 (Samtools v1.3.1); 4) Make unstranded bedGraph files from the whole reads (BEDtools v2.17.0; -bg -split); 5) Convert to Bigwig (kentUtils bedGraphToBigWig). Genome_build: TAIR10 Supplementary_files_format_and_content: Bigwig files show sequencing coverage with single base resolution (no signal smoothing or transformation were applied).
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|
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Submission date |
Apr 25, 2018 |
Last update date |
Apr 26, 2018 |
Contact name |
Maxim Ivanov |
E-mail(s) |
maxim.ivanov@plen.ku.dk
|
Organization name |
University of Copenhagen
|
Department |
Dept. of Plant and Environmental Sciences
|
Street address |
Thorvaldsensvej 40
|
City |
Frederiksberg C |
ZIP/Postal code |
1871 |
Country |
Denmark |
|
|
Platform ID |
GPL19580 |
Series (1) |
GSE113677 |
Transcription-driven Chromatin Repression of Intragenic Promoters |
|
Relations |
BioSample |
SAMN08981968 |
SRA |
SRX3994895 |