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Sample GSM4891325 Query DataSets for GSM4891325
Status Public on May 24, 2021
Title HMO-Lionel-RNA
Sample type SRA
 
Source name silvery gibbon (Hylobates moloch)
Organism Hylobates moloch
Characteristics tissue: EBV-transformed lymphocyte cell line
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
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.
 
Submission date Nov 10, 2020
Last update date May 25, 2021
Contact name Mariam Okhovat
Organization name Oregon Health and Science University
Department Medicine
Street address 3030 S Moody Ave.
City Portland
State/province Oregon
ZIP/Postal code 97239
Country USA
 
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
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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