|
| Status |
Public on Apr 07, 2021 |
| Title |
T201_S13 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
treatment: ADAR1 plasmid transfection (20 ug/T75)
|
| Treatment protocol |
Transfection (lipofectamine 3000) with increasing amounts of ADAR1 plasmid (addgene # 117928)
|
| Growth protocol |
HEK293T cells were grown and maintained in T75 flasks with DMEM complete medium (10% FBS).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolated with Monarch Total RNA purification kit (NEB) followed by two rounds of oligo-dT purification.
SMARTer® Stranded Total RNA Sample Prep Kit - Low Input Mammalian 24 reactions, (Takara Bio); standard 8-bp i5 and i7 Illumina index barcodes and adapters were added to each library. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Trimmomatic v0.36 , java -Xmx8000m -jar /sw/eicc/Pkgs/Trimmomatic/0.36/trimmomatic-0.36.jar PE -phred33 -threads 30 $a"_R1_001.fastq.gz" $a"_R2_001.fastq.gz" trimmed_data/$a"_trimmo_R1.fastq.gz" trimmed_data/singletons/$a"_trimmo_R1_singletons.fastq.gz" trimmed_data/$a"_trimmo_R2.fastq.gz" trimmed_data/singletons/$a"_trimmo_R2_singletons.fastq.gz" HEADCROP:3
STAR v2.5.2 , --genomeDir $work_dir/index --readFilesIn $a"_L001_trimmo_R1.fastq.gz" $a"_L001_trimmo_R2.fastq.gz" --runThreadN 25 --readFilesCommand zcat --sjdbGTFfile $ref_annotation_dir/genes.gtf --outSAMtype BAM SortedByCoordinate --outFilterMatchNminOverLread 0.95 --outFileNamePrefix $work_dir/mapping/$a/
Samtools v1.3, samtools index $work_dir/mapping/$a/Aligned.sortedByCoord.out.bam
Picardtools v2.0.1, java -Xmx20g -jar /sw/eicc/Pkgs/picardtools/2.0.1/picard.jar MarkDuplicates METRICS_FILE=$work_dir/mapping/$a/deleteme.metrics REMOVE_DUPLICATES=true ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT INPUT=$work_dir/mapping/$a/Aligned.sortedByCoord.out.bam OUTPUT=$work_dir/mapping/$a/unique.bam
RNAEditingIndexer script: https://github.com/a2iEditing/RNAEditingIndexer
docker run -v /home/rarthur/projects/knutson/rnaeditingindexer/full_trimmed_data/bams:/data/bams:rw -v /home/rarthur/projects/knutson/rnaeditingindexer/full_trimmed_data/indexer_output:/data/output:rw eicc/rnaeditingindexer:2019 RNAEditingIndex -d /data/bams -f .bam -l /data/output/logs_dir -o /data/output/cmpileups -os /data/output/summary_dir --genome hg38 --stranded --paired_end
Genome_build: hg38, UCSC complete, downloaded Aug 2015
|
| |
|
| Submission date |
Apr 06, 2021 |
| Last update date |
Apr 07, 2021 |
| Contact name |
Steven Douglas Knutson |
| E-mail(s) |
[email protected]
|
| Phone |
8479779677
|
| Organization name |
Emory University
|
| Department |
Chemistry
|
| Lab |
Heemstra
|
| Street address |
1515 Dickey Drive
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE171545 |
Direct Immunodetection of Global A-to-I RNA Editing Activity with a Chemiluminescent Bioassay |
|
| Relations |
| BioSample |
SAMN18630882 |
| SRA |
SRX10519508 |
