|
| Status |
Public on Nov 24, 2014 |
| Title |
HC-A13-14 |
| Sample type |
SRA |
| |
|
| Source name |
Whole lumbar spinal cord homogenate
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Healthy donor
tissue: whole lumbar spinal cord
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using mirVanaTM miRNA isolation kit (Ambion) according to the manufacturer’s protocol. RNAseq analysis was performed in Harvard genetic facility. Ribosomal reduction using Qiagen kit gene read rRNA depletion kit - http://www.qiagen.com/Products/Catalog/Assay-Technologies/Next-Generation-Sequencing/GeneRead-rRNA-Depletion-Kit#orderinginformation. Direction mRNA sequencing Integenix protocol - http://www.genome.med.harvard.edu/documents/illumina/IntegenX_Apollo324_mRNA_Seq_Protocol_10012012.pdf
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were aligned to the reference transcriptome generated from the GENCODE reference annotations version 14 using Bowtie version 0.12.9. Expression level abundances for all GENCODE genes were estimated using RSEM version 1.2.3. Differential expression analysis was done for all GENCODE genes using the DESEQ algorithm within the Trinity framework version 2013-02-25.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with FPKM reads
|
| |
|
| Submission date |
Dec 03, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Oleg Butovsky |
| E-mail(s) |
obutovsky@rics.bwh.harvard.edu
|
| Phone |
1-617-525-5313
|
| Organization name |
Brigham and Women's Hospital, Harvard Medical School
|
| Department |
Center of Neurologic Diseases
|
| Lab |
Dr. Oleg Butovsky
|
| Street address |
77 Avenue Louis Pasteur, Office 614
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE52946 |
miR-155 plays a crucial role in ALS and is an immune therapeutic target [RNA-Seq] |
| GSE52947 |
Targeting miR-155 restores abnormal microglia and attenuates disease in SOD1 mice |
|
| Relations |
| BioSample |
SAMN02429400 |
| SRA |
SRX386357 |
