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| Status |
Public on May 13, 2019 |
| Title |
sh_3495 |
| Sample type |
SRA |
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| Source name |
Peripheral blood
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| Organism |
Homo sapiens |
| Characteristics |
cell type: CD34+ HSCe
shRNA: LMNA
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| Treatment protocol |
shRNA-mediated knockdown of LMNA was performed.
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| Growth protocol |
Pre-stim type II
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| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were extracted using the Qiagen RNeasy Plus Micro kit (#74034), following the manufacturer's instructions.
Stranded paired-end libraries were prepared using the Illumina TruSeq Stranded Total RNA kit by the University of Miami Human Genomics Sequencing Core. ERCC spike-ins were included prior to ribo-depletion. Libraries were sequenced on the NextSeq 500 with 75 bp-reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Sample_22
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| Data processing |
Using Cutadapt (version 1.12), all reads were trimmed to 72 basepairs and adapters were removed.
Reads were aligned to the hg19 gencode v19 reference genome using the STAR aligner (version 2.5.2b), specifying the following parameters: outFilterType= BySJout, outFilterMultimapNmax=20, alignSJoverhangMin=8, alignSJDBoverhangMin=1 , outFilterMismatchNmax=999, alignIntronMin=20, alignIntronMax=1000000, alignMatesGapMax=1000000, alignEndsType=EndToEnd.
Gene counts were calculated using QoRTs. QoRTs was run in stranded mode using the hg19 gencode annotation file that included ERCC spike-in information, but did not include entries for ribosomal RNA, mitochondrial RNA, or tRNA.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: The processed data files are tab-delimited text files that contain the raw counts generated by QoRTs.
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| Submission date |
Jun 25, 2018 |
| Last update date |
May 15, 2019 |
| Contact name |
Maria E. Figueroa |
| E-mail(s) |
[email protected]
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| Phone |
305-243-7333
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| Organization name |
University of Miami Miller School Of Medicine
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| Department |
Human Genetics
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| Street address |
1501 NW 10th Ave, BRB 742F
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| City |
Miami |
| State/province |
Florida |
| ZIP/Postal code |
33136 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE104408 |
Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia |
| GSE116254 |
Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia (RNA-Seq of LMNA KD) |
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| Relations |
| BioSample |
SAMN09484612 |
| SRA |
SRX4297980 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3223230_Sample_22.txt.gz |
222.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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