|
| Status |
Public on Jun 13, 2019 |
| Title |
155_Donor-40_CD103neg_59 |
| Sample type |
SRA |
| |
|
| Source name |
Tumor
|
| Organism |
Homo sapiens |
| Characteristics |
cell type surface markers: CD103neg
cell type: CD45+CD3+CD8+CD103plus/minus
donor: Donor-40
|
| Treatment protocol |
NA
|
| Growth protocol |
CD8+ cell types were isolated from human tissue and directly sorted by Flow cytometry into a 96-well plate wells with lysis buffer with RNAase inhibitor (Takara) - Described in Picelli et al. Nat Protoc. 2014, PMID:24385147. No particular cell growth procedure was required.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cell RNAseq was performed as described in Picelli et al.Nat Protoc. 2014, PMID:24385147. We performed 23 cycles of amplification.
Single cell RNAseq was perfromed as described in Picelli et al.Nat Protoc. 2014, PMID:24385147. Barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina) were prepared as following manufacturer's protocol.
DNA sequencing - Libraries were sequenced on the HiSeq2500 Illumina platform to obtain 50-bp single end reads (barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina)).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Whole Transcriptome Amplification (SmartSeq2 - Picelli et al.2014)
|
| Data processing |
Single-cell RNA–seq data were mapped against the human hg19 reference genome using TopHat
Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the gene_id, http://www huber.embl.de/users/anders/HTSeq/). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
Genome_build: hg19
Supplementary_files_format_and_content: Clarke_SC_raw_counts.txt contains raw counts of sequencing reads obtained with HTSeq-count
Supplementary_files_format_and_content: Clarke_SC_TPM.txt contains contains Transcript per Million normalized counts
|
| |
|
| Submission date |
Mar 15, 2018 |
| Last update date |
Jun 13, 2019 |
| Contact name |
Pandurangan Vijayanand |
| E-mail(s) |
vijay@lji.org
|
| Organization name |
La Jolla Institute for Allergy and Immunology
|
| Department |
Division of Vaccine Discovery
|
| Lab |
VD-Vijay
|
| Street address |
9420 Athena Circle
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE111894 |
Single-cell transcriptomic analysis of tissue resident memory T cells in human lung cancer [scRNA-seq] |
| GSE111898 |
Single-cell transcriptomic analysis of tissue resident memory T cells in human lung cancer. |
|
| Relations |
| BioSample |
SAMN08718390 |
| SRA |
SRX3797802 |
