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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 01, 2017 |
| Title |
micro-dissected cells [JC58_Bl6_and_Cast] |
| Sample type |
SRA |
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| Source name |
Bone marrow small structure dissection to single-cells mapped to mm10 refseq
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| Organism |
Mus musculus |
| Characteristics |
strain: Mixed C57Bl/6 and CAST/EiJ
tissue: Bone marrow
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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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| Description |
Bone marrow small structure dissection to single-cells mapped to mm10 refseq and to a modified RefSeq containing the CAST/EiJ SNPs:
The JC57 and JC58 experiments are control experiments where we mixed, in a 1:1 ratio, bone marrow cells from two genetically different strains of mice (C57Bl/6 and CAST/EiJ). In the case of JC57 and JC58, because we blindly sampled cells that could be either from the C57Bl/6 or CAST/EiJ strain, we mapped the raw reads to both the classical RefSeq (mm10, based on C57Bl/6, here corresponding to the processed files JC57_Bl6.coutt.csv and JC58_Bl6.coutt.csv), and to a modified RefSeq containing the CAST/EiJ SNPs (here corresponding to the processed files JC57_Cast.coutt.csv and JC58_Cast.coutt.csv).
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| Data processing |
Raw data files for single-cell samples contain data for 96 multiplexed cells. Raw data for bulk samples contain data for 2000 cells processed in bulk in a single library. The column number containing the data in the bulk sample processed data refers to the barcode ID. Cell-specific bar codes are available in the file cel-seq_barcodes.csv on the series record.
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).
When indicated, reads were mapped to a modified RefSeq with inserted CAST/EiJ SNPs
Genome_build: mm10
Supplementary_files_format_and_content: *.gene.coutt.csv: 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 of 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 |
Nov 01, 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) |
| GSE89378 |
Single-cell and bulk RNA-seq of sorted and micro-dissected mouse bone marrow and fetal liver 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 |
SAMN05960678 |
| SRA |
SRX2313283 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2367690_JC58_Bl6.coutt.csv.gz |
369.8 Kb |
(ftp)(http) |
CSV |
| GSM2367690_JC58_Cast.coutt.csv.gz |
369.4 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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