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| Status |
Public on Jun 24, 2016 |
| Title |
micro-dissected cells [JC39] |
| Sample type |
SRA |
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| Source name |
Bone marrow
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| Organism |
Mus musculus |
| Characteristics |
cell type: bone marrow cells
cell subtype: micro-dissected cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were directly placed into Trizol (Life Technologies) and total RNA was isolated according to the manufacturer’s instructions, with the following alterations. RNA was precipitated overnight at -20 °C, with 2.5µg GlycoBlue (Life Technologies).
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases).
The 'cel-seq_barcodes.csv' file contains the 96 different barcodes that we used. The description of the reads structure, and how to process the fastq files, was already described in a recent paper: Grün et al. 2015, Nature, Sep 10;525(7568):251-5, in methods: quantification of transcript abundance.
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicate the cell number within the experiment, separated by a space. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.
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| Submission date |
Jan 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jean-Charles Boisset |
| E-mail(s) |
j.boisset@hubrecht.eu
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| Organization name |
Hubrecht Institute
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| Lab |
A. van Oudenaarden
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| Street address |
Uppsalalaan 8
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| City |
Utrecht |
| ZIP/Postal code |
3584CT |
| Country |
Netherlands |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE76983 |
Single-cell RNA-seq of sorted and micro-dissected mouse bone marrow cells |
| GSE89379 |
Transcriptomics of single-cell and bulk sorted and micro-dissected mouse bone marrow, fetal liver and small intestine crypt cells |
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| Relations |
| BioSample |
SAMN04422002 |
| SRA |
SRX1534993 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2041926_JC39.coutt.csv.gz |
249.5 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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