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Sample GSM2258563 Query DataSets for GSM2258563
Status Public on Aug 18, 2016
Title AB638
Sample type SRA
 
Source name gut_ILC
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 SAMN05509338
SRA SRX1997793

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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