|
| Status |
Public on Aug 18, 2016 |
| Title |
AB586 |
| Sample type |
SRA |
| |
|
| Source name |
antibiotics ILC
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
organ: Small intestine lamina propria
selection marker: CD45+CD3-CD19-GR1-B220-CD127+
treatment: vancomycin (0.5 g/l), ampicillin (1 g/l),kanamycin (1 g/l), and metronidazole (1 g/l)
developmental stage: adult
|
| Treatment protocol |
mice were given a combination of vancomycin (0.5 g/l), ampicillin (1 g/l), kanamycin (1 g/l), and metronidazole (1 g/l) in their drinking water.
|
| Growth protocol |
8 to 9 weeks-old mice housed at the Weizmann Institute animal facility
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were extracted using the lamina propria dissociation kit (Miltenyi Biotech).
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
single cell RNA-seq for gene expression quantitation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Note: Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header
|
| Data processing |
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
|
| |
|
| Submission date |
Aug 03, 2016 |
| 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 |
GPL19057 |
| Series (2) |
| GSE85152 |
The spectrum and regulatory landscapes of intestinal innate lymphoid cells are shaped by the microbiome (single cells) |
| GSE85157 |
The spectrum and regulatory landscapes of intestinal innate lymphoid cells are shaped by the microbiome |
|
| Relations |
| BioSample |
SAMN05509344 |
| SRA |
SRX1997787 |
