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| Status |
Public on Sep 19, 2017 |
| Title |
Apoe knock-out_NonPhagocytic_03 |
| Sample type |
SRA |
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| Source name |
FACS sorted MG cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: microglia
genotype: Apoe knock-out
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| Extracted molecule |
total RNA |
| Extraction protocol |
Samples (1,000 FACS-sorted FCRLS+ microglia cells) were lysed in TCL buffer.
Smart-Seq2 libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform. cDNA libraries were generated from sorted cells using the Smart-seq2 protocol (Picelli et al., 2013). RNA sequencing was performed using Illumina NextSeq500 using a High Output v2 kit to generate 2 x 25 bp reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
KO 03 NP
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| Data processing |
Transcripts were quantified by the BTL computational pipeline using Cuffquant version 2.2.1(Trapnell et al., 2012). The BTL’s internal QC pipeline utilizes Mm10 (UCSC Link) and GENCODE mouse genome (GRCm38), version 9 (Ensembl 84) annotations. Reads are demultiplexed on a third Illumina read, and then each sample’s sequences are aligned utilizing STAR v2.4.2a. Alignments are then processed using Picard v1.1073 tools to add read groups and other sequencing information via AddOrReplaceReadGroups, reorder the BAM file to the reference via ReorderSam, and mark duplicate sequences via MarkDuplicates. After this, the pipeline gathers summary metrics via the following Picard commands: CollectAlignmentSummaryMetrics, QualityScoreDistribution, CollectReadGCMetrics, MeanQualityByCycle, CollectInsertSizeMetrics. Genes are then quantified using RSEM v1.2.21 (Li, et. al) with the paired-end option. The data is then assessed for quality using RNA-SeQC (Deluca, et. al.). Raw counts were normalized using TMM normalization and then log2-transformed. Batch effects were corrected using removeBatchEffect from the R package limma (v. 3.28.21). Supplementary_files_format_and_content: FPKM and TPM values of gene expression from RNA-seq data in tab-delimited text format.
Supplementary_files_format_and_content: tab-delimited text files include FPKM and TPM values for each Sample
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| Submission date |
Aug 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Oleg Butovsky |
| E-mail(s) |
obutovsky@rics.bwh.harvard.edu
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| Phone |
1-617-525-5313
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| Organization name |
Brigham and Women's Hospital, Harvard Medical School
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| Department |
Center of Neurologic Diseases
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| Lab |
Dr. Oleg Butovsky
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| Street address |
77 Avenue Louis Pasteur, Office 614
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE101689 |
The TREM2-APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases |
| GSE102564 |
The TREM2-APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases VI |
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| Relations |
| BioSample |
SAMN07500194 |
| SRA |
SRX3089324 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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