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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 08, 2020 |
| Title |
NEU 1157 |
| Sample type |
SRA |
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| Source name |
peripheral blood
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| Organism |
Mus musculus |
| Characteristics |
cell type: neutrophils
strain: C57BL6
developmental stage: adult
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| Extracted molecule |
total RNA |
| Extraction protocol |
After Ficoll separation of peripheral blood, neutrophils were collected from the cell pellet following red cell lysis
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 |
neutrophil
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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 |
SAMN13750524 |
| SRA |
SRX7517168 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4255680_1157.tsv.gz |
2.3 Mb |
(ftp)(http) |
TSV |
| GSM4255680_1157minus.mm10.bw |
154.2 Mb |
(ftp)(http) |
BW |
| GSM4255680_1157plus.mm10.bw |
156.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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