|
| Status |
Public on May 05, 2024 |
| Title |
Grey matter line 3 |
| Sample type |
SRA |
| |
|
| Source name |
Brain gray matter
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Brain gray matter
cell type: Grey matter line
cell isolation: LCM isolated cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was normalized to 100 pico grams prior to oligo-dT capture and cDNA synthesis with Takara’s SMART-Seq v4. The resulting cDNA was assessed on the Fragment Analyzer with the High Sense Large Fragment kit and quantified using a Life Technologies’ Qubit 3.0 fluorometer.
Libraries were generated using Illumina’s Nextera XT DNA Library Prep kit. Medium depth sequencing (>30 million reads per sample) was performed with an Illumina HiSeq 2500 on a Rapid Run v2, 125 base pairs, Paired End run.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
GM_line_3
|
| Data processing |
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2 fastq software
After investigating the quality of the raw data, sequence read was trimmed to remove possible adapter sequences and nucleotides with poor quality using cuadapt
The trimmed reads were mapped to the human reference genome (GRCh38) using the HISAT2.
We employed DESeq2 to normalized raw counts with median of ratios methods after filtering >10 reads per gene and to determine the differentially expressed genes and pathways from comparisons.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
|
| |
|
| Submission date |
Feb 07, 2024 |
| Last update date |
May 05, 2024 |
| Contact name |
Jihye Kim |
| E-mail(s) |
kim.jihey@gmail.com
|
| Phone |
7209755448
|
| Organization name |
Cleveland Clinic
|
| Department |
Quantitative Health Sciences
|
| Street address |
9500 Euclid Ave.
|
| City |
Cleveland |
| State/province |
Ohio |
| ZIP/Postal code |
44195 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE255290 |
Transcript Profiles of Microglia/Macrophage Cells at the Borders of Chronic Active and Subpial Gray Matter Lesions in Multiple Sclerosis |
|
| Relations |
| BioSample |
SAMN39860062 |
| SRA |
SRX23567028 |
