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Sample GSM3106842 Query DataSets for GSM3106842
Status Public on Jun 15, 2019
Title RNA-seq_human primary fetal astrocytes_rep1
Sample type SRA
 
Source name human primary fetal astrocytes
Organism Homo sapiens
Characteristics cell type: human primary fetal astrocytes
Growth protocol Human primary fetal astrocytes were cultured according to the ScienCell protocol (catalog #1801).
Extracted molecule total RNA
Extraction protocol RNA was extracted using the RNeasy Mini Kit (QIAGEN #74104) according to its protocol.
The TruSeq Stranded mRNA protocol from Illumina was followed for library construction (catalog #RS-122-2101).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description LM014
Data processing All reads were quality trimmed using TrimGalore 0.4.5 prior to further processing. For libraries having undergone paired-end sequencing, only the first read was used.
Reads were mapped using STAR and GENCODE V19 transcripts were quantified with RSEM using the standard ENCODE parameters.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: tab-delimited text files including gene expression estimates from RSEM and signal tracks in bigwig format
 
Submission date Apr 20, 2018
Last update date Jun 17, 2019
Contact name Yin Shen
E-mail(s) Yin.Shen@ucsf.edu
Phone 4155023403
Organization name UCSF
Department Department of Neurology
Lab Shen Lab
Street address 513 Parnassus Ave
City SAN FRANCISCO
State/province CALIFORNIA
ZIP/Postal code 94143-0410
Country USA
 
Platform ID GPL20301
Series (2)
GSE113482 Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes [RNA-Seq]
GSE113483 Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes
Relations
BioSample SAMN08965069
SRA SRX3981939

Supplementary file Size Download File type/resource
GSM3106842_LM014.genes.results.txt.gz 1.4 Mb (ftp)(http) TXT
GSM3106842_astrocyte.rna-seq.minus.bigwig 201.4 Mb (ftp)(http) BIGWIG
GSM3106842_astrocyte.rna-seq.plus.bigwig 209.3 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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