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Series GSE69132 Query DataSets for GSE69132
Status Public on Jun 30, 2015
Title Integrated genomics of Crohn’s disease risk variant identifies a role for CLEC12A in antibacterial autophagy
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Using integrated genomics we identify a role for CLEC12A in antibacterial autophagy. Clec12a-/- mice are more susceptible to bacterial infection and CLEC12A deficient cells exhibit impaired antibacterial autophagy. We used transcriptional profilinf to understand the role of CLEC12A in the response to Salmonella and Listeria.
Overall design Bone marrow-derived macrophages from WT or Clec12a-/- mice were infected with Salmonella enterica serovar Typhimurium or Listeria monocytogenes. Cells were harvested at 0,3,6, and 24hours post-infection for RNA analysis.

Please note that single-end sequencing was performed but two files: R1 files that contained the sample barcodes (19 or 17bp reads) and R2 files that contained the single-end-sequenced 46bp cDNA reads were generated. Since the barcode info is mostly redundant, only R2 reads were submitted (described in 'raw_file_readme.txt').
Contributor(s) Lassen K, Goel G, Xavier RJ
Citation(s) 26095365
Submission date May 21, 2015
Last update date May 15, 2019
Contact name Ramnik J Xavier
Organization name Massachusetts General Hospital
Street address 185 Cambridge Street
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (42)
GSM1693734 WT_BMDMs_T0_rep1
GSM1693735 WT_BMDMs_T0_rep2
GSM1693736 WT_BMDMs_T0_rep3
BioProject PRJNA284662
SRA SRP058617

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE69132_KL.Clec12a.DESEQ2_Normalization.rLog.UMI.txt.gz 2.4 Mb (ftp)(http) TXT
GSE69132_raw_file_readme.txt 5.5 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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