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| Status |
Public on Jan 23, 2018 |
| Title |
blood case indiv 2 |
| Sample type |
SRA |
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| Source name |
Ashmatic_peripheral blood
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| Organism |
Homo sapiens |
| Characteristics |
disease status: Ashmatic
tissue: peripheral blood
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Nasal epithelial cells were collected from behind the inferior turbinate with a cytology brush using a nasal illuminator. Whole blood was collected using PAXgene RNA blood tubes. RNA was isolated using PAXgene RNA blood extraction kits.
Poly(A) selected RNA-seq libraries (n=38) were constructed using 500 ng of blood and nasal airway epithelial total RNA from 9 atopic asthmatics and 10 non-atopic controls. Libraries were constructed and barcoded with the Illumina TruSeq RNA Sample Preparation v2 protocol. Barcoded nasal airway RNA-seq libraries from each of the 19 subjects were pooled and sequenced as 2 x 100bp paired-end reads across two flow cells of an Illumina HiSeq 2000. Barcoded blood RNA-seq libraries from each of the 19 subjects were pooled and sequenced as 2 x 100bp paired end reads across 4 lanes of an Illumina Hiseq 2000 flow cell.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
SF14
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| Data processing |
We mapped reads onto the human transcriptome (Ensembl GRCh37) and genome reference (Ensembl hg19) using TopHat2 (v 2.0.13) with the default parameters. TopHat2 was supplied with a set of known transcripts (as a GTF formatted file, Ensembl GRCh37) using –G option.
The mapped reads of each sample are stored in a binary format (.bam). ROP (gprofile.py) categorizes the reads into genomic categories (junction read, CDS, intron, UTR3, UTR5, introns, inter-genic read, deep a deep inter-genic read, mitochondrial read, and multi-mapped read) based on their compatibility with the features defined by Ensembl (GRCh37) gene annotations.
ROP (rprofile.py) categorizes reads into repeat elements (classes and families) based on their compatibility with repeat instances defined by RepeatMasker annotation (RepeatMasker v3.3, Repeat Library 20120124).
We count the number of reads overlapping variable(V), diversity (D), joining (J), and constant (C) gene segments of B cell receptor (BCR) and T cell receptor (TCR) loci using htseq-count (HTSeq v0.6.1).
We remapped the remaining unmapped reads to the human reference genome (hg19) and transcriptome (known transcripts, Ensembl GRCh37) using Megablast (BLAST+ 2.2.30).
The remaining unmapped reads were mapped to the reference repeat sequences using Megablast (BLAST+ 2.2.30). The reference repeat sequences were downloaded from Repbase v20.07 (http://www.girinst.org/repbase/). Human repeat elements (humrep.ref and humsub.ref) were merged into a single reference.
. We used IgBlast (v. 1.4.0) with a stringent e-value threshold (e-value < 10-20) to map the remaining unmapped reads onto the V(D)J gene segments of the of the B cell receptor (BCR) and T cell receptor (TCR) loci. Gene segments of B cell receptors (BCR) and T cell receptors (TCR) were imported from IMGT version: 3.1.17 (International ImMunoGeneTics information system). The IMGT database contains: variable (V) gene segments; diversity (D) gene segments; and joining (J) gene segments.
We used Megablast (BLAST+ 2.2.30) to align remaining unmapped reads onto the collection of bacterial, viral, and eukaryotic reference genomes. Bacterial and viral genomes were downloaded from NCBI (ftp://ftp.ncbi.nih.gov/). Genomes of eukaryotic pathogens were downloaded from EuPathDB (http://eupathdb.org/eupathdb/). We used MetaPhlAn2 (Metagenomic Phylogenetic Analysis, v 2.0) to obtain the taxonomic profile of microbial communities present in the sample.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: BLAST Tabular Output (more details provided in the readme.txt)
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| Submission date |
Jan 17, 2018 |
| Last update date |
Jan 24, 2018 |
| Contact name |
Harry Taegyun Yang |
| E-mail(s) |
harry2416@gmail.com
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| Organization name |
University of California, Los Angeles
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| Department |
Computer Science
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| Lab |
Eleazar Eskin Lab
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| Street address |
Engineering VI 286
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE109313 |
ROP: Dumpster Diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues |
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| Relations |
| BioSample |
SAMN08370513 |
| SRA |
SRX3587729 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2937079_SF14_bacteria.out.txt.gz |
3.4 Mb |
(ftp)(http) |
TXT |
| GSM2937079_SF14_immune.out.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
| GSM2937079_SF14_repeat.out.txt.gz |
2.9 Mb |
(ftp)(http) |
TXT |
| GSM2937079_SF14_virus.out.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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