|
Status |
Public on Aug 18, 2016 |
Title |
AB721 |
Sample type |
SRA |
|
|
Source name |
gut_ILC_NoGFP
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 organ: Small intestine lamina propria selection marker: CD45+CD3-CD19-GR1-B220-CD127+ treatment: None 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 |
SAMN05509375 |
SRA |
SRX1997814 |