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| Status |
Public on Jan 26, 2019 |
| Title |
RMM104 |
| Sample type |
SRA |
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| Source name |
Fat
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| Organism |
Mus musculus |
| Characteristics |
cell type: Fat3 Lyve1-
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Arcturus PicoPure RNA Isolation kit (Thermofisher, KIT0204) according to manufacturer’s protocol.
cDNA libraries were prepared using 2ng of total RNA and 1ul of a 1:50,000 dilution of Ambion ERCC RNA Spike-in Controls (Thermofisher, 4456740) using the SMARTSeq v2 protocol described in Nature Protocols volume 9, pages 171-181 (Picelli et al., 2014) with the following modifications: 1. Use of 20mM TSO, 2. Use of 250pg of cDNA with 1/5 reaction of Nextera XT kit (Illumina, FC-131). 31 samples were subjected to an indexed PE sequencing run of 2x51 cycles on an Illumina HiSeq 2000 (20-24 samples/lane)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Run featureCounts on every bam file using Gencode annotation, to assign mapped sequencing reads to Ensembl gene IDs.
Join together all the counts outputs of featureCounts into a unique matrix of raw counts.
Perform TMM (trimmed mean of M-values) scale normalization on the DGEList.
Calculate RPKM (Reads Per Kilobase of transcript per Million mapped reads) of TMM-normalized counts.
Genome_build: mm7
Supplementary_files_format_and_content: Tab-delimited text files include log2 RPKM values for each Sample
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| Submission date |
Jan 25, 2019 |
| Last update date |
Jan 26, 2019 |
| Contact name |
Florent Ginhoux |
| E-mail(s) |
Florent_Ginhoux@immunol.a-star.edu.sg
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| Organization name |
Singapore Immunology Network (SIgN), A*STAR
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| Street address |
8A Biomedical Grove, Immunos Building, Level 3
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| City |
Singapore |
| ZIP/Postal code |
138648 |
| Country |
Singapore |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE125667 |
Two distinct interstitial macrophage populations coexist across tissues in unique subtissular niches [FACs sorted] |
| GSE125691 |
Two distinct interstitial macrophage populations coexist across tissues in unique subtissular niches |
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| Relations |
| BioSample |
SAMN10820194 |
| SRA |
SRX5292115 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3579886_RMM104.txt.gz |
300.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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