|
| Status |
Public on Jan 08, 2022 |
| Title |
1uM_GSK591_SKaTER_2_days_+DRB_(10_min)_Rep_1 |
| Sample type |
SRA |
| |
|
| Source name |
A549
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
rna population: nascent RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Poly(A) RNA seq: RNA was extracted using RNeasy® Mini Kit (Qiagen, 74104) following the manufacturer’s protocol. SKaTER-seq: RNA was isolated using TRIzol (Thermo, 15596026) at -80 °C. RNA isolation was followed by poly(A)-depletion using the NEBNext Poly(A) mRNA magnetic isolation mod-ule (NEB, E7490L).
Poly(A) RNA seq: Stranded RNA seq libraries were constructed by Novogene Genetics US. The barcoded libraries were sequenced by Novogene on an Illumina platform using 150nt paired end libraries generating ~30-40 million reads per replicate. SKaTER-seq: Stranded RNA-seq libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) and KAPA Unique Dual-Indexed Adapters (Roche) according to instructions provided by the manufacturer.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Library strategy: SKaTER-seq
Adapter trimming accomplished with trim_galore v0.6.5 (trim_galore --paired -j 8 $file ${fn}_2.fastq.gz)
Alignment performed with STAR v2.4.2a (STAR --genomeDir $GENDIR --readFilesIn ${fn}_1_val_1.fq.gz ${fn}_2_val_2.fq.gz --readFilesCommand zcat --outFileNamePrefix ${fn}_ --runThreadN 12 --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outSAMattributes All --outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0.51 --outFilterMatchNminOverLread 0.51 --outFilterMismatchNmax 4 --alignIntronMax 50000 --sjdbGTFfile $GENDIR/genes.gtf --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic)
Duplicate control Picard tools 2.3.0 (java -jar `which picard.jar` MarkDuplicates INPUT=${fn}_Aligned.sortedByCoord.PEonly.bam OUTPUT=${fn}_Aligned.sortedByCoord.PEonly_marked.bam METRICS_FILE=${fn}_Aligned.sortedByCoord.PEonly_marked_metrics CREATE_INDEX=true)
Splicing analysis rMATs v4.0.2 (rmats.py --b1 $fn --b2 $file --gtf gencode.v19.annotation.gtf --od ${file%.txt} --tmp ${file%.txt}_tmp -t single --readLength 150 --nthread 35)
Genome_build: hg19
Supplementary_files_format_and_content: SKaTER aligned reads are provided as bigwig files generated using deepTools v3.3.1 (bamCoverage -b $file -o ${fn}.bw -p 35 -bs 1 -v --ignoreDuplicates). rMATS summary files are rMATs JCEC output concatenated into a single text file for each condition.
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| |
|
| Submission date |
Dec 17, 2020 |
| Last update date |
Jan 09, 2022 |
| Contact name |
David Shechter |
| E-mail(s) |
[email protected]
|
| Phone |
7184304120
|
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Biochemistry
|
| Street address |
1300 Morris Park Ave., Forchheimer 304
|
| City |
Bronx |
| State/province |
New York |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE163421 |
Type I and II PRMTs Inversely Regulate Post-Transcriptional Intron Detention through |
|
| Relations |
| BioSample |
SAMN17104621 |
| SRA |
SRX9698359 |
