|
| Status |
Public on Mar 06, 2022 |
| Title |
Vero E6 cell replicate 2 DM(-) |
| Sample type |
SRA |
| |
|
| Source name |
Host cell
|
| Organism |
Chlorocebus sabaeus |
| Characteristics |
group: cell
treatment: Not demethylase treated
molecule subtype: ncRNA, tRNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extracted RNA was reverse transcribed. Following RT, products were ligated to adaptors. These adaptors were captured on beads and pooled and underwent demethylase and/or CMC treatment. Following this, samples were submitted for illumine sequencing.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw fastq files were demultiplexed based on a barcode on the first 4nt of read2. We used Je suite demultiplexer with the following parameters: je demultiplex F1=FastQ/$sample$R1 F2=FastQ/$sample$R2 BF=$bar_code_path  BPOS=BOTH BM=READ_2 LEN=6:4 O=./0_barcode_read2/$sample FORCE=true C=false
Reads were then mapped to reference genome using bowtie2 and the following parameters: bowtie2 -x $reference -U $bar_directory$sample$in1   -S ./3_bowtie2/$index_file/$sample_dir$underscore$sample$suffix -q -p 10 --local —no-unal  Several reference genomes were used, as indicated in the text and processed file descriptions
Sam files were used to generate several processed files using a variety of tools
For 'pileup' summary files, sam files were covered to bam files and sorted using samtools command samtools view -bS -o ./4_bam_sort_wig/$index_file/$base.bam ./3_bowtie2/$index_file/$filename and samtools sort ./4_bam_sort_wig/$index_file/$base.bam -o ./4_bam_sort_wig/$index_file/$base.sort.bam Next bam files were compressed with IGV command igvtools count -z 5 -w 1 -e 250 --bases 4_bam_sort_wig/$index_file/$base.sort.bam 4_bam_sort_wig/$index_file/$base.wig $reference to make summary .wig files. Wig files were reformatted with custom python scripts (available on GitHub)
For 'counts' reads, custom python script using the pysam python wra for samtools was used to tally the number of reads mapping to each reference sequence.
For tRNA fragment analysis, the pysam python package wrapper for samtools was used to determine the 3primeposition for each read and organize reads into separate sam files based on this position. These separate sam files were processed to generate pileup and count files as previously described
Genome_build: For Sars-Cov2 genome, we used NCBI NC_0455122_Wuhan_seafood_market_pneumonia_virus_isolate_Wuhan_Hu_1_complete_genome. For SRP mapping we used ensemble genome GCA_000409795.2. For vero cell tRNA refernce, we used tRNAs from RFAM set, then used tRNAscanSE to filter for tRNAs with scores > 70
Supplementary_files_format_and_content: see file: processed_data_file_names_and_descriptions.xlsx (available on the series record).
Supplementary_files_format_and_content: Some processed data files contain no data because we did not identify fragments from these tRNA positions present within our samples. However, we opted to include them still within our larger data set because when you run the custom python script and process step to identify these fragments, these are our files and we wanted to include our comprehensive result.
|
| |
|
| Submission date |
Aug 26, 2021 |
| Last update date |
Mar 06, 2022 |
| Contact name |
Tao Pan |
| E-mail(s) |
taopan@uchicago.edu
|
| Phone |
(773) 702-4179
|
| Organization name |
University of Chicago
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
929 E. 57th Street
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL28895 |
| Series (1) |
| GSE182883 |
Profiling selective packaging of host RNA and viral RNA modification in the SARS-CoV-2 virion |
|
| Relations |
| BioSample |
SAMN21013292 |
| SRA |
SRX11931932 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5542480_CsabaeusncRNA_count_TP-CK-16S-CW01_S4L1_bc2_TCTG.tsv.gz |
10.7 Kb |
(ftp)(http) |
TSV |
| GSM5542480_CsabaeustRNA_count_TP-CK-16S-CW01_S4L1_bc2_TCTG.tsv.gz |
2.7 Kb |
(ftp)(http) |
TSV |
| GSM5542480_CsabaeustRNA_count_TP-CK-16S-CW01_S4L1_bc2_TCTG_-1_0_.tsv.gz |
99 b |
(ftp)(http) |
TSV |
| GSM5542480_CsabaeustRNA_count_TP-CK-16S-CW01_S4L1_bc2_TCTG_-2_-1_.tsv.gz |
2.7 Kb |
(ftp)(http) |
TSV |
| GSM5542480_CsabaeustRNA_count_TP-CK-16S-CW01_S4L1_bc2_TCTG_0_10_.tsv.gz |
99 b |
(ftp)(http) |
TSV |
| GSM5542480_CsabaeustRNA_count_TP-CK-16S-CW01_S4L1_bc2_TCTG_10_20_.tsv.gz |
100 b |
(ftp)(http) |
TSV |
| GSM5542480_CsabaeustRNA_count_TP-CK-16S-CW01_S4L1_bc2_TCTG_20_30_.tsv.gz |
1.7 Kb |
(ftp)(http) |
TSV |
| GSM5542480_CsabaeustRNA_count_TP-CK-16S-CW01_S4L1_bc2_TCTG_30_40_.tsv.gz |
2.2 Kb |
(ftp)(http) |
TSV |
| GSM5542480_CsabaeustRNA_count_TP-CK-16S-CW01_S4L1_bc2_TCTG_40_50_.tsv.gz |
1.7 Kb |
(ftp)(http) |
TSV |
| GSM5542480_CsabaeustRNA_count_TP-CK-16S-CW01_S4L1_bc2_TCTG_50_60_.tsv.gz |
2.0 Kb |
(ftp)(http) |
TSV |
| GSM5542480_CsabaeustRNA_count_TP-CK-16S-CW01_S4L1_bc2_TCTG_60_200_.tsv.gz |
2.6 Kb |
(ftp)(http) |
TSV |
| GSM5542480_CsabaeustRNA_pileup_TP-CK-16S-CW01_S4L1_bc2_TCTG.tsv.gz |
204.4 Kb |
(ftp)(http) |
TSV |
| GSM5542480_CsabaeustRNA_pileup_TP-CK-16S-CW01_S4L1_bc2_TCTG_-1_0_.tsv.gz |
15.8 Kb |
(ftp)(http) |
TSV |
| GSM5542480_CsabaeustRNA_pileup_TP-CK-16S-CW01_S4L1_bc2_TCTG_-2_-1_.tsv.gz |
204.1 Kb |
(ftp)(http) |
TSV |
| GSM5542480_CsabaeustRNA_pileup_TP-CK-16S-CW01_S4L1_bc2_TCTG_20_30_.tsv.gz |
61.3 Kb |
(ftp)(http) |
TSV |
| GSM5542480_CsabaeustRNA_pileup_TP-CK-16S-CW01_S4L1_bc2_TCTG_30_40_.tsv.gz |
94.4 Kb |
(ftp)(http) |
TSV |
| GSM5542480_CsabaeustRNA_pileup_TP-CK-16S-CW01_S4L1_bc2_TCTG_40_50_.tsv.gz |
66.4 Kb |
(ftp)(http) |
TSV |
| GSM5542480_CsabaeustRNA_pileup_TP-CK-16S-CW01_S4L1_bc2_TCTG_50_60_.tsv.gz |
84.6 Kb |
(ftp)(http) |
TSV |
| GSM5542480_CsabaeustRNA_pileup_TP-CK-16S-CW01_S4L1_bc2_TCTG_60_200_.tsv.gz |
167.7 Kb |
(ftp)(http) |
TSV |
| GSM5542480_CsabeausncRNA_pileup_TP-CK-16S-CW01_S4L1_bc2_TCTG.tsv.gz |
1.4 Mb |
(ftp)(http) |
TSV |
| GSM5542480_sarscov2Genome_count_TP-CK-16S-CW01_S4L1_bc2_TCTG.tsv.gz |
117 b |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
