|
| Status |
Public on Jun 13, 2019 |
| Title |
Clarke_Bulk_Donor-14_NIL_CD103pos |
| Sample type |
SRA |
| |
|
| Source name |
Non-involved lung
|
| Organism |
Homo sapiens |
| Characteristics |
cell type surface markers: CD45+CD3+CD4-CD8+CD103plus/minus
cell type: Lymphocyte
donor #: Donor-14
|
| Treatment protocol |
Were noted samples were stimulated with 4 hours of PMA/ionomycine treatment, otherwise sampled were directly ex-vivo
|
| Growth protocol |
Cell types were isolated from tissue samples and directly sorted by Flow cytometry into trizol or lysis buffer. No particular cell growth procedure was required.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA-seq was performed as described previously by Seumois et al 2016 and Ganesan et al 2017 using smart-seq2 method with 0.5ng of total RNA. Total RNA was purified using a miRNAeasy kit (Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
Barcoded Illumina sequencing libraries were sonstructed as per the protocol described by illumina (Nextera XT library preparation kit, Illumina).
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 (Smart-seq2 - Picelli et al.2014)
|
| Data processing |
Bulk RNA–seq data were mapped against the human hg19 reference genome using TopHat (v2.0.9 , (--library-type fr-unstranded --no-coverage-search
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_Bulk_raw-counts.txt contains raw counts of sequencing reads obtained with HTSeq-count
Supplementary_files_format_and_content: Clarke_Bulk_TPM.txt 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) |
| GSE111892 |
Single-cell transcriptomic analysis of tissue resident memory T cells in human lung cancer [ bulk RNA-seq] |
| GSE111898 |
Single-cell transcriptomic analysis of tissue resident memory T cells in human lung cancer. |
|
| Relations |
| BioSample |
SAMN08718003 |
| SRA |
SRX3797689 |
