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| Status |
Public on Nov 21, 2014 |
| Title |
A683 |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Homo sapiens |
| Characteristics |
case id: Case 15
classification: Control
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| Treatment protocol |
Fresh-frozen brain tissue was pulverized in liquid nitrogen, lysed in QIAzol and homogenized using QIAshredder columns.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the miRNeasy Kit (Qiagen) according to the manufacturer's protocol
small RNA cDNA library according to Hafner et al, Methods, 2012, and Hafner et al., RNA, 2011
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Samples are demultiplexed by assigning by 5 nt barcodes and adapters and barcodes are removed from fastq files converted to fasta using perl scripts.
Fasta file is collapsed into a non-redundant fasta file in which the read count is contained within the read header and mapped against an in-house ncRNA reference derived from GenBank and an internally curated set of miRNAs. BWA v0.5.9 used, with parameters aln -n 2 -t 16 -i 0 -d 0 to align reads to the reference.
Multi-mapping reads are first assigned to hits with the lowest number of errors, then the count is split equally between the number of locations mapped.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated file summarizing reads attributed to an internal reference of ncRNAs. First column is the read, second is the count, last column a comma-separated list of mapped annotation
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| Submission date |
Nov 20, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ismael Santa Maria |
| E-mail(s) |
is2395@columbia.edu
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| Phone |
212-305-6371
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| Organization name |
Columbia University
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| Department |
Pathology & Cell Biology
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| Lab |
15-401
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| Street address |
630W 168TH STREET
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE63501 |
Dysregulation of microRNAs in neurodegeneration |
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| Relations |
| BioSample |
SAMN03202913 |
| SRA |
SRX764715 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1551183_A683_geo.txt.gz |
6.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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