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| Status |
Public on Jul 06, 2015 |
| Title |
GATA2_GMP_WT_1 |
| Sample type |
SRA |
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| Source name |
GATA2-transduced GMP (48 hrs)
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: wild type
growth protocol: FACS purified, transduced, resorted and cultured for 48 hrs
library construction: SMARTer UltraTMLow Input RNA Kit, then TruSeq sample preparation kit IP-202-1012
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq sample preparation kit (IP-202-1012) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina's CASAVA1.8.2 software was used for basecalling
The reads that passed illumina's quality/purity filter were aligned to the mouse genome (Illumina iGenomes mm9 build) using STAR aligner (version 2.3.0) with default parameters.
The resulting SAM alignment files were then converted to the BAM file format, sorted and indexed using SAMtools (version 0.1.14).
The HTSeq python package (Anders S, Pyl PT, and Huber W. 2014. Bioinformatics) was used to summarize the aligned sequence reads into counts by feature using the "union" setting.
The DESeq bioconductor package was used to statistically analyze raw count data from HTSeq for differential expression (Anders S, Huber W.. 2010. Genome Biology)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw count values
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| Submission date |
Feb 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Sarah Bettigole |
| E-mail(s) |
[email protected]
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| Organization name |
Weill Cornell Medical College
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| Street address |
1300 York Avenue, E907
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE65753 |
Analysis of wildtype and Xbp1-deficient hematopoietic progenitor cell transcriptomes |
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| Relations |
| BioSample |
SAMN03333423 |
| SRA |
SRX869265 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1604074_GATA2_GMP1_WT.txt.gz |
92.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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