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Sample GSM4494851 Query DataSets for GSM4494851
Status Public on Nov 19, 2020
Title HT22-R-anti-HSF1-LR_1
Sample type SRA
 
Source name HT-22 cells
Organism Mus musculus
Characteristics tissue: Hippocampal cell line
passages: 4
strain: N/A
Treatment protocol 200,000 HT22 cells treated with anti-HSF1 LNA (150nM) or scramble (50uM) LNA for 24h, following treatment with 30uM (final concentration) of amyloid beta peptides (42/ 1-42 aa) or a control peptide with an inverted amino acid sequence (R/ reverse 42-1) dissolved in DMSO. Cells grown in 6 well plated (1mL growth media).
Growth protocol The HT-22 hippocampal cell line was grown as a monolayer up to 70% confluency in DMEM, 1% pen/strep, 10%Calf Serum (heat inactivated)
Extracted molecule total RNA
Extraction protocol Trizol RNA extraction: 1mL trizol added to pelleted cells, dissolved 5min. 200uL chloroform added to trizol treated cells, incubate 2min. Centrifuged at 12 000xg 4C. Aqueous layer treated with 500uL isopropanol, incubate -20C 1hour, centrifuged at 12 000xg 10min 4C, pellet washed with 75% ethanol and centrifuged at 7 500xg 5min 4C. Pellet dried 1min, resuspended in 30uL pure H2O
Libraries prepared as described before (Zovoilis et al, Cell 2016) and in the manuscript that accompanies the current submission. Enrichemnt of short RNAs was done using a modified protocol for the MiRvana size selection kit. Short-RNA-seq library performed using NEBNext Multiplex Small Library Prep E7560S and a customized bead cleaning approach to get rid of very small fragments (miRNAs) and adapter dimers. Long-RNA-seq library performed after fragmentation and ribosomal RNA depletion with NEBNext rRNA depletion kit using NEBNext Ultra RNA Library Prep Kit for Illumina (E7530)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description long-RNA
Data processing Quality of the sequenced reads was estimated using FASTQC from the Babraham Institute (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Trimming of adapter sequences was performed using cutadapt-1.18 (DOI: http://dx.doi.org/10.14806/ej.17.1.200) with standard Illumina adaptor sequences
Mapping small RNA-seq reads to UCSC mm10 using bwa-0.7.17 (PMID: 19451168) single end mode, with aln option and default parameters. Mapping long RNA-seq reads to ensembl GRCm38 primary assembly using hisat2-2.1.0 (PMID: 31375807) single end mode, with parameters: --dta -k 1.
Conversion of bam files to genomic coordinates was done using bedtools-2.26.0 (PMID: 20110278). For small RNA-seq, in house python scripts were implemented to construct an accumulation model around a hypothetical common Transcription Start Site (TSS) for all B2 elements. For long RNA-seq, FPKM and TPM for genes were generated using StringTie-1.3.4d (PMID: 25690850), with annotation: ensembl GRCm38 patch 94 gff3 file.
Genome_build: mm10
Supplementary_files_format_and_content: B2_count files for short-RNA-seq reads: 5' end read count per position across the B2 loci metagene, constructed by aligning to the start position all B2 loci identified by RepeatMasker (mm1a,mm1t, mm2 repeat names). CSV file inlcudes two columns with column one representing the position from the metagene start and column two representing the counts of the 5' ends of each read mapping to these B2 RNAs. Gene_abund files for long-RNA-seq reads, tab delimited text files contain FPKM and TPM values for genes calculated by stringtie.
 
Submission date Apr 23, 2020
Last update date Nov 19, 2020
Contact name Athanasios Zovoilis
Organization name University of Lethbridge
Street address University of Lethbridge -Chemistry and Biochemistry, 4401 University Drive W
City Lethbridge
State/province Alberta
ZIP/Postal code T1K6T5
Country Canada
 
Platform ID GPL13112
Series (1)
GSE149243 Increased processing of SINE B2 non coding RNAs unveils a novel type of transcriptome de-regulation underlying amyloid beta neuro-pathology
Relations
BioSample SAMN14681410
SRA SRX8167601

Supplementary file Size Download File type/resource
GSM4494851_gene_abund_HT22-R-anti-HSF1-LR_1.tab.gz 1.2 Mb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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