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| Status |
Public on May 18, 2017 |
| Title |
Control_Cd3+Cd4+_1 |
| Sample type |
SRA |
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| Source name |
t cell
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| Organism |
Mus musculus |
| Characteristics |
tissue: blood
cell type: t cell
genotype: wild type
co-culture status: freshly isolated from tissue
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| Treatment protocol |
All cell populations were purified via FACS. Purity mask was applied.
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| Extracted molecule |
total RNA |
| Extraction protocol |
At least 100 ng of total RNA from both freshly harvested and cultured cells was isolated (phenol-chloroform separation of TRIzol LS) and purified using Qiagen’s RNeasy Mini Kit.
RNA library preps were prepared and multiplexed using Illumina’s TruSeq RNA Library Preparation Kit v2 (non-stranded and poly-A selection) and 10 nM of cDNA was used as input for high-throughput sequencing via Illumina’s HiSeq 2500 producing 51 bp paired-end reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Sample_RL_15
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| Data processing |
Base calling and sequencing reads de-multiplexing were performed using bcl2fastq v2.17.
Sequencing reads were checked for quality (FastQC v0.11.5), and trimmed/filtered using Trimmomatic v0.36.
Read alignment to the transcriptome sequence reference of the UCSC mm10 genome build were performed using TopHat2 v2.1.0.
Mapped reads were assembled into transcripts, and abundance measures (FPKM values) quantified using Cufflinks v2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: Single tab-delimited data-matrix with GENE_ID, GENE_DESCRIPTION, and SAMPLE_NAMES. All numerical inputs represent FPKM values.
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| Submission date |
Nov 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Balvir Kunar, Jr. |
| E-mail(s) |
bak2010@med.cornell.edu
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| Organization name |
Weill Cornell Medical College
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| Department |
Regenerative Medicine; Physiology, Biophysics, & Systems Biology
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| Lab |
Shahin Rafii, M.D.
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| Street address |
1300 York Ave
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| City |
New York City |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE88840 |
Conversion of adult endothelium to immunocompetent haematopoietic stem cells |
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| Relations |
| BioSample |
SAMN05981610 |
| SRA |
SRX2327525 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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