|
| Status |
Public on Oct 28, 2016 |
| Title |
Nexabiotic#1 |
| Sample type |
SRA |
| |
|
| Source name |
SI-LP
|
| Organism |
Mus musculus |
| Characteristics |
cell type: CD4+ T cells
bacterial species: Nexabiotic
strain: C57BL/6
age: 6 weeks
Sex: Male
phenotype markers: CD4+ TCRb+ CD45+ DAPI-
|
| Treatment protocol |
Germ-free mice were left unmanipulated or colonized with different bacterial species for 2 weeks prior to sacrifice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted into TCL buffer (Qiagen #1031576) + 2-Mercaptoethanol (Sigma-Aldrich# M6250) and then processed according to the Smart-Seq2 protocol by the Broad Technology Labs
The Smart-Seq2 protocol was performed by the Broad Technology Labs
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Data was separated by barcode and aligned using Tophat version 2.0.10 with default settings.
Transcripts were quantified using the Cufflinks suite version 2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts
|
| |
|
| Submission date |
Oct 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
CBDM Lab |
| E-mail(s) |
cbdm@hms.harvard.edu
|
| Phone |
617-432-7747
|
| Organization name |
Harvard Medical School
|
| Department |
Microbiology and Immunobiology
|
| Lab |
CBDM
|
| Street address |
77 Avenue Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE89261 |
Transcriptional response of small-intestinal lamina propria CD4+ T cells to bacterial colonization |
|
| Relations |
| BioSample |
SAMN05949066 |
| SRA |
SRX2276611 |
