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Sample GSM3110985 Query DataSets for GSM3110985
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.
 
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).
 
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

Supplementary file Size Download File type/resource
GSM3110985_s5_ssrp1_TSS-Seq_biorep1_Minus.bw 3.1 Mb (ftp)(http) BW
GSM3110985_s5_ssrp1_TSS-Seq_biorep1_Plus.bw 3.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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