|
| Status |
Public on Aug 23, 2020 |
| Title |
21_540_CD4_GFPneg |
| Sample type |
SRA |
| |
|
| Source name |
CD4 positive T Cells
|
| Organism |
Homo sapiens |
| Characteristics |
subjectid: S540
Sex: male
culture: CD4
egfp: GFPneg
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sorted populations were stored in 350l of RLT buffer with 1% of 2-Mercaptoethanol (BME) at -80°C, purified using Qiagen RNeasy Micro columns, and RNA quality was assessed using an Agilent Bioanalyzer.
Ten nanograms of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the Illumina NexteraXT DNA Library Preparation kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
616_Michelle_CD4-CD4CD8_DESeq2_NormCounts.txt
|
| Data processing |
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the human (GRCh38) genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).
|
| |
|
| Submission date |
Apr 26, 2019 |
| Last update date |
Aug 23, 2020 |
| Contact name |
Gregory K Tharp |
| E-mail(s) |
[email protected]
|
| Phone |
404-727-7797
|
| Organization name |
Yerkes National Primate Research Center
|
| Department |
Developmental and Cognitive Neuroscience
|
| Lab |
Genomics Core
|
| Street address |
954 Gatewood Dr
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30329-4208 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE130368 |
Innate, non-cytolytic CD8+ T cell-mediated suppression of HIV replication by MHC-independent inhibition of virus transcription |
|
| Relations |
| BioSample |
SAMN11515472 |
| SRA |
SRX5758338 |
