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Status |
Public on May 24, 2021 |
Title |
HMO-Lionel-RNA |
Sample type |
SRA |
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Source name |
silvery gibbon (Hylobates moloch)
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Organism |
Hylobates moloch |
Characteristics |
tissue: EBV-transformed lymphocyte cell line
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using the mirVana™ Total RNA Isolation kit (ThermoFisher Scientific) following the manufacturer's instructions on each EBV-transformed lymphocyte cell line. High-quality RNA was subjected to llumina Tru-seq stranded total RNA library preparation, including Ribo-depletion. The Qubit dsDNA High Sensitivity kit (Thermo Fisher Scientific) and Agilent Bioanalyzer 2100 were used to QC the libraries.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Data processing |
DATA PROCESSING STEPS TO GENERATE THE '*_summary.txt' FILES: Raw reads were trimmed using Trimmomatic to remove adaptor sequences, as well as low quality and short reads (2:30:10:26:true SLIDINGWINDOW:4:20 TRAILING:20 LEADING:20 MINLEN:50). Trimmed RNA-seq libraries were annotated using RepeatMasker version 4.0.3. The gibbon (Hylobates sp.) 20150807 Repbase library was used for annotation. We used a custom script to group repeats in each library based on repeat class and family, and to calculate the %count and %length (of total repeats) they constituted. Supplementary_files_format_and_content: Text files (*_summary.txt) summarizing the %count and %length of each repeat, repeat family and repeat class of the annotated RNA-seq reads.
DATA PROCESSING STEPS TO GENERATE THE '*_mapped.fasta.out_summary.txt' FILES: The Burrow's Wheeler Aligner bwa-mem algorithm was used to map RNA-seq reads to de novo assembled contigs generated from CENP-A, CENP-B, and CENP-C ChIP-sequencing data. Reads that successfully aligned to the de novo assemblies were extracted using SAMtools and converted to FASTA format using Bedtools and Seqtk. Repeats in the subsequent processed FASTA files were annotated using RepeatMasker version 4.0.3. The gibbon (Hylobates sp.) 20150807 Repbase library was used for annotation. We used a custom script to group repeats in each library based on repeat class and family, and to calculate the %count and %length (of total repeats) they constituted. Supplementary_files_format_and_content: Text files (*_mapped.fasta.out_summary.txt) summarizing the %count and %length of each repeat, repeat family and repeat class of the annotated RNA-seq reads.
DATA PROCESSING STEPS TO GENERATE THE '*-RM-summary.txt' FILES: RNA-seq library reads were mapped to the Nleu3.0 genome using the Burrows-Wheeler Aligner bwa-mem algorithm. Unaligned reads, assumed to contain centromere-derived reads, were separated using SAMtools and converted to FASTA format using Bedtools and Seqtk. Next, we used the Burrow's Wheeler Aligner bwa-mem algorithm to map the unaligned reads to de novo assembled contigs generated from CENP-A, CENP-B, and CENP-C ChIP-sequencing data. Reads that successfully aligned to the de novo assemblies, assumed to be enriched for centromere-derived reads, were extracted using SAMtools and converted to FASTA format using Bedtools and Seqtk. Repeats in the subsequent processed FASTA files were annotated using RepeatMasker version 4.0.3. The gibbon (Hylobates sp.) 20150807 Repbase library was used for annotation. We used a custom script to group repeats in each library based on repeat class and family, and to calculate the %count and %length (of total repeats) they constituted. Genome_build: Nleu3.0 Supplementary_files_format_and_content: Text files (*-RM-summary.txt) summarizing the %count and %length of each repeat, repeat family and repeat class of the annotated RNA-seq reads.
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Submission date |
Nov 10, 2020 |
Last update date |
May 25, 2021 |
Contact name |
Mariam Okhovat |
Organization name |
Oregon Health and Science University
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Department |
Medicine
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Street address |
3030 S Moody Ave.
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City |
Portland |
State/province |
Oregon |
ZIP/Postal code |
97239 |
Country |
USA |
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Platform ID |
GPL29394 |
Series (2) |
GSE161191 |
Comparative analyses of gibbon centromeres reveal dynamic species-specific shifts in repeat composition [RNA-seq] |
GSE161217 |
Comparative analyses of gibbon centromeres reveal dynamic species-specific shifts in repeat composition |
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Relations |
BioSample |
SAMN16725392 |
SRA |
SRX9470018 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4891325_HMORNASeq-UnmappedGenomeMappedRepARK-CENPA-RM-summary.txt.gz |
2.5 Kb |
(ftp)(http) |
TXT |
GSM4891325_HMORNASeq-UnmappedGenomeMappedRepARK-CENPB-RM-summary.txt.gz |
2.6 Kb |
(ftp)(http) |
TXT |
GSM4891325_HMORNASeq-UnmappedGenomeMappedRepARK-CENPC-RM-summary.txt.gz |
2.9 Kb |
(ftp)(http) |
TXT |
GSM4891325_HMORNA_vs_HMORepARKCENPA_mapped.fasta.out_summary.txt.gz |
9.2 Kb |
(ftp)(http) |
TXT |
GSM4891325_HMORNA_vs_HMORepARKCENPB_mapped.fasta.out_summary.txt.gz |
10.0 Kb |
(ftp)(http) |
TXT |
GSM4891325_HMORNA_vs_HMORepARKCENPC_mapped.fasta.out_summary.txt.gz |
10.4 Kb |
(ftp)(http) |
TXT |
GSM4891325_Lionel-RNA-RM-R1_summary.txt.gz |
61.9 Kb |
(ftp)(http) |
TXT |
GSM4891325_Lionel-RNA-RM-R2_summary.txt.gz |
63.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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