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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jan 08, 2020 |
Title |
MON 1208 |
Sample type |
SRA |
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Source name |
peripheral blood
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Organism |
Mus musculus |
Characteristics |
cell type: monocytes (Gr-1+Mac-1+) strain: C57BL6 developmental stage: adult
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Extracted molecule |
total RNA |
Extraction protocol |
After Ficoll separation of peripheral blood, monocytes (Gr-1+Mac-1+) were sorted from the mononuclear fraction. Total RNA was extracted using TRIzol and the Ambion PureLink RNA Mini Kit (Life Technologies, cat# 12183018), treated with DNase to remove genomic DNA using the DNAfree Kit (Life Technologies, cat# AM1906). Sequencing libraries were constructed from 100 ng of DNase-treated, total RNA using the ScriptSeqv2 Complete Kit (Illumina cat# BHMR1224). The RNA depleted for rRNA using the Ribo-Zero removal reagents and fragmented. First strand cDNA was then synthesized using a 5’ tagged random hexamer and reverse transcription, followed by annealing of a 5’ tagged, 3’-end blocked terminal-tagged oligo and second strand synthesis. The Di-tagged cDNA fragments were purified, barcoded, and PCR-amplified for 15 cycles.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Description |
monocyte
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Data processing |
Illumina's bcl2fastq2 to generate fastq files The sequence reads were processed using the ENCODE3 long RNA-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL002LPE/). In brief, reads were mapped to the mouse genome using STAR, followed by RSEM for gene quantifications using Gencode vM4 genes. UCSC's wigToBigWig to convert wiggle track Genome_build: mm10 Supplementary_files_format_and_content: bigWig, signal from STAR Supplementary_files_format_and_content: tsv, expression levels from RSEM
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Submission date |
Jan 07, 2020 |
Last update date |
Jan 08, 2020 |
Contact name |
Ross Hardison |
E-mail(s) |
rch8@psu.edu
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Organization name |
Pennsylvania State University
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Street address |
303 Wartik Lab
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City |
University Park |
State/province |
PA |
ZIP/Postal code |
16802 |
Country |
USA |
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Platform ID |
GPL19057 |
Series (2) |
GSE143261 |
An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis [RNA-seq] |
GSE143271 |
An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis |
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Relations |
BioSample |
SAMN13750527 |
SRA |
SRX7517165 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4255677_1208.tsv.gz |
2.3 Mb |
(ftp)(http) |
TSV |
GSM4255677_1208minus.mm10.bw |
70.9 Mb |
(ftp)(http) |
BW |
GSM4255677_1208plus.mm10.bw |
70.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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