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| Status |
Public on Apr 27, 2017 |
| Title |
NBB2009-005 |
| Sample type |
SRA |
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| Source name |
non-demented without AD-like pathology (healthy controls)
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| Organism |
Homo sapiens |
| Characteristics |
diagnosis: non-demented
presents ad pathology: No
tissue: superior temporalis gyrus
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the SPLIT RNA extraction kit (Lexogen GmbH, Vienna, Austria) yielding the large RNA fraction with a lower cut-off size of 150 nt. Evaluation on an Bioanalyzer RNA Nano chip (Agilent Technologies) showed medium to high RNA quality (RIN of 6.2 – 8.3).
Briefly, 4 µg Terminator-treated RNA was full-length reverse transcribed, and 1/20th of the purified cDNA was then amplified in one of 12 parallel PCR reactions. Each PCR reactions was set up with one universal 5’ primer and a 3’ primer selective for one of the 12 possible combinations of the two terminal nucleotides of the mRNA body, immediately upstream of the poly(A) tail. 200 ng of all 288 PCR products (24 RNA samples amplified separately in 12 matrix fields) were heat-fragmented and then ligated to SOLiD-compatible adapters. The libraries were PCR amplified in 17 cycles, with PCR primers indexing each sample with one out of 96 bar-codes. Three lane mixes were created, each from 96 libraries corresponding to 24 samples amplified in 4 matrix fields, dedicating equal molarities to each of the libraries. The three lane mixes SOR04 (selective 3’ primer nucleotides AC, AG, CA, GT), SOR05 (AA, AT, CC, CG) and SOR06 (CT, GA, GC, GG) were then further size-selected on a Pippin Prep automated gel elution system (Sage Biosciences, Beverly, MA, USA) in the range of 170 to 400 bp.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500xl Genetic Analyzer |
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| Description |
Sample 14
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| Data processing |
Sequence and quality files, in Lifetech proprietary .xsq binary format, were mapped against the GRGCh37/hg19 version of the Homo sapiens genome using the Lifetech Lifescope 2.5.1 whole Transcriptome analysis pipeline. Additional details for read alignment are provided in the readme.txt.
Tables of read counts per gene were generated from the alignments using the HTSEQ package.
Genome_build: GRGCh37/hg19
Supplementary_files_format_and_content:
Gene_list.txt: List of associated RefSeq gene names corresponding to rows in Sample*.txt files (see below).
Sample*.txt files contain RPKM values of genes for each of the SQUARE matrix fields. Each field represents a transcript with one of the 12 different ending dinucleotides: 'AC, AG, CA, GT, CT, GA, GC, GG, AA, AT, CC, CG'. Columns correspond to matrix fields, Rows correspond to genes according to Gene_list.txt file, Gene list order is identical to all Sample*.txt files and the first row is the 12 SQUARE ending dinucleotides.
NormMatrix.txt: Scaling factor based on the mean PCR field yield after patient normalization. These values should be used normalize RPKM values per patient per field.
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| Submission date |
Apr 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Shahar Barbash |
| E-mail(s) |
barbashshahar@gmail.com
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| Organization name |
The Rockefeller University
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| Lab |
Tom Sakmar
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| Street address |
1230 York Ave
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL16288 |
| Series (1) |
| GSE57152 |
Alternative poly(A) in Alzheimer's disase |
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| Relations |
| BioSample |
SAMN02739915 |
| SRA |
SRX528858 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1376265_Sample14.txt.gz |
367.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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