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| Status |
Public on Jun 28, 2021 |
| Title |
CHLA02 |
| Sample type |
SRA |
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| Source name |
CHLA 02
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Atypical Teratoid Rhabdoid Tumor
cell line: CHLA 02
technical replicate: No
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| Growth protocol |
Cells were grown under conditions recommended by ATCC (www.atcc.org); in DMEM:F12 Medium (ATCC 30-2006) with 20 ng/mL human recombinant EGF, 20 ng/mL human recombinant basic FGF, and B-27 Supplement (Invitrogen, Cat. No.17504) to a final concentration of 2% (v/v).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy plus kit (Qiagen, USA) according to the manufacturer’s instruction.
Libraries were prepared and sequenced at NISC (www.nisc.nih.gov). The Illumina TruSeq Stranded Total RNA protocol was used in accordance with manufacturers instructions (Illumina, San Diego, CA). Stranded 125bp paired-end (Illumina HiSeq 2500).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Atypical Teratoid Rhabdoid Tumor (ATRT)
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| Data processing |
RTA 1.13.48 and CASAVA 1.8.2. software was used for basecalling and deplexing. Post deplexing, quality of the sequence data generated was inspected using the FastQC tool (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) followed by use of the Trimmomatic tool (http://www.usadellab.org/cms/?page=trimmomatic) to clip away adaptor sequence, 5' bias, and/or low quality sequence that might be present. Surviving read pairs were then mapped against the current instance of the human genome (ftp.ensembl.org/pub/release-82/fasta/homo_sapiens/dna/) two separate times using the "RNA-Seq" tool found within the CLCbio Genomics Workbench (www.clcbio.com) under default parameters. For the first mapping, expression for ensembl annotated transcripts (ftp.ensembl.org/pub/release-82/gtf/homo_sapiens/Homo_sapiens.GRCh38.82.chr.gtf.gz) was specified to be enumerated in TPM (Transcript Per Million) units. For the second mapping, expression was specified to also be enumerated in TPM units but this time for RepeatMasker "LTR" annotated features (http://www.repeatmasker.org/). These enumerated values were then imported into R (cran.r-project.org) and analyzed separately by mapping. To start, TPM units were pedestalled by 2, Log2 transformed, filtered to remove transcripts/features not having at least one transformed value >1, then quantile normalized. Post normalization, quality of the data was challenged and confirmed by Tukey box plot, covariance-based PCA scatter plot, and Pearson correlation heat map. To remove noise-biased expression, lowess modeling was performed across libraries (CV ~ mean expression) and the resulting fit inspected for the lowest expression value where the linear relationship between CV and mean expression was observed to be grossly lost. Expression values for a transcript/feature less than this value were subsequently construed to be noise-biased and floored to equal this value. Transcripts/Features not having at least one library with an expression greater than this value were then discarded as not detected. Expression for transcripts/features not discarded between libraries representing technical replicates were also collapsed using the max observed value per transcript/feature respectively. Where after, relationships across libraries were evaluated using expression for transcripts/features via clustered heat map (heatmap.2) and circos plot (RCircos).
Genome_build: GRCh38.82
Supplementary_files_format_and_content: Tab-delimited text files containing TPM expression counts for ensembl annotated transcripts and RepeatMasker "LTR" annotated features.
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| Submission date |
Dec 20, 2018 |
| Last update date |
Jun 28, 2021 |
| Contact name |
Kory R Johnson |
| E-mail(s) |
johnsonko@ninds.nih.gov
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| Phone |
301-402-1956
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| Organization name |
NINDS/NIH
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| Department |
DIR IT & Bioinformatics
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| Lab |
Bioinformatics Section
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| Street address |
10/3B01, 9000 Rockville Pike
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE124210 |
HERV-K ENV expression is a therapeutic target in atypical teratoid rhabdoid tumors |
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| Relations |
| BioSample |
SAMN10621028 |
| SRA |
SRX5171119 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3525744_CHLA02_Ensembl_Transcript_TPM_Expression.txt.gz |
7.0 Mb |
(ftp)(http) |
TXT |
| GSM3525744_CHLA02_RepeatMasker_LTR_TPM_Expression.txt.gz |
11.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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