|
| Status |
Public on Aug 08, 2014 |
| Title |
CD4 |
| Sample type |
SRA |
| |
|
| Source name |
T CD4+ cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
organ: Spleen
selection marker: B220-, CD3+, CD19-, CD4+, CD8-
treatment: none
cell type: T CD4+ cells
|
| Treatment protocol |
Samples were extracted from unrteated, C57BL/6 female wild-type mice.
|
| Growth protocol |
12 to 15 weeks-old mice housed at the Weizmann Institute animal facility
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Each mouse was euthanized and either leg bones or spleen, or both, removed, homogenized to single cell suspension, red cells removed by selective lysis.
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Sample 11
3' RNA-seq for digital gene expression quantitation
|
| Data processing |
single end protocol ( some samples used read2 to read molecule barcodes only)
Illumina Casava1.8 software used for basecalling.
alignment: bowtie2 with deafult parameters
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
Quantifying RNA expression in genes: analyzeRNA.pl rna mm9 -d <tag directory> -norm 1e7 (HOMER)
Genome_build: mm9
Supplementary_files_format_and_content: 1256271tableS2.txt is a tab-delimited expression matrix that includes mRNA molecule count values for each Sample
|
| |
|
| Submission date |
Aug 05, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ido Amit |
| E-mail(s) |
ido.amit@weizmann.ac.il
|
| Phone |
972-8-9343338
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Immunology
|
| Street address |
234 Herzl st.
|
| City |
Rehovot |
| ZIP/Postal code |
760001 |
| Country |
Israel |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE60101 |
Chromatin state dynamics during blood formation (RNA-Seq) |
| GSE60103 |
Chromatin state dynamics during blood formation |
|
| Relations |
| Reanalyzed by |
GSE80797 |
| BioSample |
SAMN02952070 |
| SRA |
SRX669492 |
